title: lib46612_CE2E7ANXX

status: Public on Feb 11 2022

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: CD8 enriched, CD8+ T cells

extract_protocol:
At 0, 0.5, 2, 6, and 24 hours, cells from a single donor and time point were mixed into one tube and then sorted into each individual (CD4+/CD8+ and stimulation condition) population on a BD FACS Aria Fusion into lysis buffer. Coding in this way was done to decrease time variability which would be most sensitive in earlier time points.  SMARTseq v4 chemistry was used to generate cDNA following the manufacturer's instructions.
Reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.  Sequencing libraries were constructed using a modified protocol of the Nextera XT DNA Sample Preparation Kit (Illumina) to generate Illumina-compatible barcoded libraries
Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS Kits (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: Fresh PBMC were enriched to either effector/memory CD4+ by adding anti-CD62L in the CD4 antibody cocktail, or terminal effector/memory CD8+ by adding CD197 and CD45RA antibodies to the CD8 antibody cocktail. Cells were washed before adding microbeads. Non-target cells were magnetically separated in columns from the untouched flow though.  Prior to plating, the memory T cells were stained with viability dye (Invitrogen) in PBS, then with anti-CD4 or anti-CD8 with a unique fluorochrome designating its combination for cell population and stimulation condition. Cells were then plated with 4 stimulations: (1) OKT3 (anti-CD3) + human IgG (2) OKT3 + MAdCAM-1 (3) OKT3 + MAdCAM-1+ vedolizumab (4) OKT3 + anti-CD28. Plates were briefly centrifuged to place cells in contact with stimuli. At 0, 0.5, 2, 6, and 24 hours, cells from a single donor and time point were mixed into one tube and then sorted into each individual (CD4+/CD8+ and stimulation condition) population on a BD FACS Aria Fusion into lysis buffer for SMARTseq. Coding in this way was done to decrease time variability which would be most sensitive in earlier time points.

tag: individual

tag: stimulation

value: MADCAM + vedolizumab + anti-CD3

tag: timepoint

value: CD8+ T cells

tag: sequencing batch


title: lib46611_CE2E7ANXX

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

country: USA

institute: Benaroya Research Institute

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: hIgG1 + anti-CD3

tag: cell type


title: lib46610_CE2E7ANXX


title: lib46608_CE2E7ANXX


title: lib46606_CE2E7ANXX


title: lib46607_CE2E7ANXX


title: lib46604_CE2E7ANXX

value: anti-CD28 + anti-CD3


title: lib46602_CE2E7ANXX


title: lib46603_CE2E7ANXX


title: lib46599_CE2E7ANXX


title: lib46601_CE2E7ANXX


title: lib46597_CE2E7ANXX


title: lib46598_CE2E7ANXX


title: lib46600_CE2E7ANXX


title: lib46596_CE2E7ANXX

source_name: CD4 enriched, CD4+ T cells

value: CD4+ T cells


title: CD4 Naïve T cells of wildtype control, replicate1 [WT_forKO_CD4_Na_rep1]

status: Public on Feb 28 2022

data_processing:
library strategy: Bulk RNA Barcoding and sequencing (BRB-seq)
Reads were demultiplexed by BRBseqTools (v1.3.1)
Reads were mapped using STAR (v2.7.6a, --outFilterMultimapNmax 1)
Mapped reads were counted by BRBseqTools (v1.3.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

organism: Mus musculus

source_name: CD4 Naïve T cells of wildtype control

extract_protocol:
CD4 and CD8 Naive T cells were sorted from spleen using antibodies against CD8a, CD19, CD4, CD3e, CD62L, CD45R/B220, CD44, and CD16.
Total RNA from sorted cells was isolated by using RNeasy plus micro (QIAGEN, 74034). 50 ng for each sample was used for the reverse transcription with barcoded primer BU3 followed by the purification, second strand synthesis and tagmentation following the original BRB-seq protocol (Alpern et al., 2019 Genome Biology) but using AMPure XP for purification.

value: CD4 Naive T cells

tag: strain/genotype

tag: replicate


title: lib46130_CDT4VANXX

value: MADCAM + anti-CD3


title: lib46594_CE2E7ANXX


title: lib46132_CDT4VANXX


title: CD8 Naïve T cells of Bach2<18del>, replicate1 [KO_CD8_Na_rep1]

source_name: CD8 Naïve T cells of Bach2<18del>

value: CD8 Naive T cells


title: lib46595_CE2E7ANXX


title: lib46128_CDT4VANXX


title: lib46127_CDT4VANXX


title: lib46125_CDT4VANXX


title: lib46126_CDT4VANXX


title: lib46124_CDT4VANXX


title: lib46605_CE2E7ANXX


title: lib46120_CDT4VANXX


title: lib46117_CDT4VANXX


title: lib46118_CDT4VANXX


title: lib46116_CDT4VANXX


title: lib46115_CDT4VANXX


title: lib46114_CDT4VANXX


title: lib46111_CDT4VANXX


title: lib46110_CDT4VANXX


title: lib46108_CDT4VANXX


title: lib46107_CDT4VANXX


title: lib46104_CDT4VANXX


title: lib46103_CDT4VANXX


title: lib46102_CDT4VANXX


title: lib46106_CDT4VANXX


title: lib46099_CDT4VANXX


title: lib46123_CDT4VANXX


title: lib46094_CDT4VANXX


title: lib46096_CDT4VANXX


title: lib46095_CDT4VANXX


title: lib46098_CDT4VANXX


title: lib46122_CDT4VANXX


title: lib46119_CDT4VANXX


title: lib46109_CDT4VANXX


title: lib46091_CDT4VANXX


title: lib46093_CDT4VANXX


title: lib46088_CDT4VANXX


title: lib46087_CDT4VANXX


title: lib46085_CDT4VANXX


title: lib46112_CDT4VANXX


title: lib46084_CDT4VANXX


title: lib46080_CDT4VANXX


title: lib46083_CDT4VANXX


title: lib46079_CDT4VANXX


title: lib46078_CDT4VANXX


title: lib46101_CDT4VANXX


title: lib46077_CDT4VANXX


title: lib46076_CDT4VANXX


title: lib46072_CDT4VANXX


title: lib46070_CDT4VANXX


title: lib46068_CDT4VANXX


title: BACH2-B1-NS_S17

library_source: genomic

data_processing:
CRISPResso (version 2.0.29)68 was used to count the genotypes of each of the base editor-induced mutations present within the sequencing data associated with each FACS sorting bin.
The read counts and genotypes for each sorting bin and the unsorted cells as output by CRIPSResso, were input into R, and MAUDE (version 0.99.3)69 was used to infer the expression levels of genotype, separately for each experiment.
Here, we assumed that 10.5% of the cells were sorted into each of the sorting bins, which was the approximate number observed to fall into each bin during the experiments. We used MAUDE's 'findGuideHitsAllScreens' function to identify the mean expression associated with each genotype (treating genotypes as MAUDE "guides"), using default parameters.
The statistical effect of rs72928038 base edits compared to WT on BACH2 expression were calculated using a paired (by experiment) one-sided Student's t-test with unequal variance.
Genome_build: GRCh37
Supplementary_files_format_and_content: Allele frequency table

molecule: genomic DNA

source_name: Jurkat T cells

growth_protocol: Jurkat T cells Cells were grown at 37 °C maintaining cultures between 1x10^5 and 1x10^6 cells per mL.

extract_protocol:
rs72928038 region amplicon libraries were prepared by nested PCR of each sample, splitting each into two 50 μL reactions (25 μL NEBNext Master Mix, 2.5 μL 10 μM BACH2_gDNAamp_F and 2.5 10 μM BACH2_gDNAamp_R, and 20 μL of reverse-crosslinked sample), program: 98 °C for 30 s, 23 cycles of 98 °C for 15 s, 65 °C for 30 s, 72 °C for 1 min, then 72 °C for 2 min, followed by 1.5X Ampure XP cleanup, and elution in 25 μL EB.
A second 50 μL PCR was performed to add Nextera adapters (25 μL NEBNext Master Mix, 2.5 μL 10 μM BACH2_gseq_F and 2.5 10 μM BACH2_gseq_R, and 20 μL of Ampure-cleaned PCR1), program: 98 °C for 30 s, 6 cycles of 98 °C for 15 s, 64 °C for 30 s, 72 °C for 30 s, then 72 °C for 2 min, followed by 1.5X Ampure XP cleanup, and elution in 25 μL EB. A final 50 μL PCR to add Nextera barcodes and sequencing adapters was then performed (25 μL NEBNext Master Mix, 2.5 μL of mixed 10 μM barcoded Nextera_F and Nextera_R, and 22.5 μL Ampure-cleaned PCR2) for 6 cycles; program: 98 °C for 30 s, 25 cycles of 98 °C for 15 s, 62 °C for 15 s, 72 °C for 16 s, then 72 °C for 2 min. The libraries were then quantified by Qubit and TapeStation, mixed at equimolar ratios, PhiX (Illumina, FC-110-3001) was added at 20%, and samples were sequenced aiming to get >1,000,000 reads per bin, on either an Illumina Nextseq 550 or MiSeq.

tag: locus

tag: sort bin

value: Not sorted


title: lib46067_CDT4VANXX


title: lib46061_CDT4VANXX


title: lib46063_CDT4VANXX


title: lib46064_CDT4VANXX


title: lib46092_CDT4VANXX


title: lib46060_CDT4VANXX


title: lib46062_CDT4VANXX


title: lib46059_CDT4VANXX


title: lib46086_CDT4VANXX


title: lib46053_CDT4VANXX


title: lib46055_CDT4VANXX


title: lib46051_CDT4VANXX


title: lib46057_CDT4VANXX


title: lib46050_CDT4VANXX


title: lib46054_CDT4VANXX


title: lib46049_CDT4VANXX


title: lib46052_CDT4VANXX


title: lib46046_CDT4VANXX


title: lib46045_CDT4VANXX


title: lib46048_CDT4VANXX


title: lib46075_CDT4VANXX


title: lib46069_CDT4VANXX


title: lib46043_CDT4VANXX


title: lib46042_CDT4VANXX


title: lib46044_CDT4VANXX


title: lib46041_CDT4VANXX


title: lib46058_CDT4VANXX


title: lib46040_CDT4VANXX


title: lib46038_CDT4VANXX


title: lib46035_CDT4VANXX


title: lib46037_CDT4VANXX


title: lib46039_CDT4VANXX


title: lib46036_CDT4VANXX


title: lib46034_CDT4VANXX


title: lib46032_CDT4VANXX


title: lib46033_CDT4VANXX


title: lib46047_CDT4VANXX


title: WT_IL rep1

status: Public on Jan 28 2022

city: Pittsburgh

first: Shanshan

last: Song

state: PA

address: 3501 Fifth Ave

institute: University of Pittsburgh

data_processing:
Adapter sequences, low quality reads, and contamination of ribosomal RNA (rRNA) and mitochondrial DNA (mtDNA) were removed prior to alignment to the mouse genome (mm10) using the STAR aligner (2.5.3a) in Partek Flow 8.0 software (Partek, USA).
Quantification was performed by annotation to the mouse genome and DESeq2 was performed for the differentially expressed gene (DEG) analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: microglial cells

growth_protocol: in vivo

extract_protocol:
Animals were perfused with saline, and hemispheric brains were collected for microglial isolation, using MACS with P2RY12 antibody.
RNA libraries were prepared with the SMARTer stranded total RNA pico V2 kit and sequenced on an Illumina HiSeqX platform

treatment_protocol: Animals were injected with tamoxifen at least 30 days prior to MCAO surgeries. Cells were isolated at 72h post-MCAO.

tag: genotype

value: Cx3cr1-CreER+/-; Nhe1+/+

tag: disease state

value: post-ischemic stroke

tag: hemisphere

value: ipsilateral hemisphere


title: KO_IL rep2

value: Cx3cr1-CreER+/-; Nhe1f/f


title: WT_IL rep2


title: WT_IL rep3


title: KO_CL rep3

value: contralateral hemisphere


title: WT_CL rep3


title: WT_CL rep2


title: KO_IL rep3


title: KO_CL rep2


title: WT_CL rep1


title: KO_IL rep1


title: KO_CL rep1


title: lib47523: 4.Stim.none.Input

status: Public on Jan 20 2022

data_processing:
Library strategy: Ribo-seq
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCm38.91
Gene counts were generated using HTSeq-count (v0.4.1)29. Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: spleen and lymph nodes

growth_protocol: cultured in T cell media (RPMI-1640, 10% Fetal Bovine Serum, 2mM GlutaMAXtm-I, 100U/mL Penicillin-Streptomycin, 55μM 2-Mercaptoethanol, 1mM Sodium Pyruvate, 1X Non-Essential Amino Acids, 10mM HEPES)

extract_protocol:
Samples were subject to either hemagluttanin IP (for RiboTag samples) or sucros fractionation (for SPEED) before RNA was isolated. Samples were either kept in -80C at this point or proceeded with standard Trizol-mediated RNA extraction protocol or the Direct-zol 96 kit (Zymo Research, R2054) was used following the on-column DNA digestion protocol.
Sequencing libraries were constructed from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and NexteraXT DNA sample preparation kit (Illumina) to generate Illumina- compatible barcoded libraries.
cDNA libraries construction used the SMARTseq v4 Ultra-Low Input kit (Clontech)

treatment_protocol: For Treg suppression assays, indicated numbers of nTregs (CD4+YFP+) and 1 x 105 CD4 Teff cells (CD4+CD25-) were cultured in round-bottom 96-well plate for the indicated times with 4 x 104 anti-CD3/CD28 coated magnetic beads (Teff:beads = 2.5:1). To control for T cell density, control cultures were cultured with either the same number of total Teff cells as in the Teff:Treg co-culture conditions or in some cases, CD4+YFP-CD45.1+ Teff cells sorted from Foxp3YFP-Cre mice were used.

tag: tissue

value: spleen and lymph nodes

value: anti-CD3/CD28 beads

tag: fraction

value: Input

tag: assay type

value: SPEED

tag: mouse id

value: CD4 Teff


title: lib47521: 3.Stim.HHT.Input

value: anti-CD3/CD28 beads HHT for 10min before harvest


title: lib47519: 3.Stim.none.Input


title: lib47518: 3.Unstim.none.Input

value: Untreated


title: lib47516: 2.Stim.Treg.Input

value: anti-CD3/CD28 beads with Tregs


title: lib47515: 2.Stim.none.Input


title: lib47520: 3.Stim.Treg.Input


title: lib47514: 2.Unstim.none.Input


title: lib47513: 1.Stim.HHT.Input


title: lib47517: 1.Stim.HHT.Input


title: lib47510: 1.Unstim.none.Input


title: lib47512: 1.Stim.Treg.Input


title: lib47511: 1.Stim.none.Input


title: lib47522: 4.Unstim.none.Input


title: lib47509: 4.Stim.Treg.Pol

value: Pol


title: lib47502: 3.Stim.HHT.SubPol

value: SubPol


title: lib47507: 4.Stim.none.Pol


title: lib47501: 3.Stim.Treg.Pol


title: lib47508: 4.Stim.Treg.SubPol


title: lib47505: 4.Unstim.none.Pol


title: lib47524: 4.Stim.Treg.Input


title: lib47498: 3.Stim.none.SubPol


title: lib47499: 3.Stim.none.Pol


title: lib47496: 3.Unstim.none.SubPol


title: lib47504: 4.Unstim.none.SubPol


title: lib47500: 3.Stim.Treg.SubPol


title: lib47495: 2.Stim.HHT.Pol


title: lib47494: 2.Stim.HHT.SubPol


title: lib47493: 2.Stim.Treg.Pol


title: lib47506: 4.Stim.none.SubPol


title: lib47490: 2.Stim.none.SubPol


title: lib47491: 2.Stim.none.Pol


title: lib47488: 2.Unstim.none.SubPol


title: lib47487: 1.Stim.HHT.Pol


title: lib47485: 1.Stim.Treg.Pol


title: lib47484: 1.Stim.Treg.SubPol


title: lib47482: 1.Stim.none.SubPol


title: lib47489: 2.Unstim.none.Pol


title: lib47486: 1.Stim.HHT.SubPol


title: lib47503: 3.Stim.HHT.Pol


title: lib47483: 1.Stim.none.Pol


title: lib47481: 1.Unstim.none.Pol


title: lib47480: 1.Unstim.none.SubPol


title: lib47497: 3.Unstim.none.Pol


title: lib38418: Ribo Treg IP_5

value: Ribo IP

value: cross of B6N.129-Rpl22tm1.1Psam/J and B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ

value: RiboTag


title: lib38416: Ribo Treg IP_3


title: lib38413: Ribo Treg input_5


title: lib38417: Ribo Treg IP_4


title: lib38410: Ribo Treg input_2


title: lib38414: Ribo Treg IP_1


title: lib38415: Ribo Treg IP_2


title: lib38407: Ribo Stim IP_4


title: lib47492: 2.Stim.Treg.SubPol


title: lib38409: Ribo Treg input_1


title: lib38408: Ribo Stim IP_5


title: lib38412: Ribo Treg input_4


title: lib38406: Ribo Stim IP_3


title: lib38411: Ribo Treg input_3


title: lib38403: Ribo Stim input_5


title: lib38401: Ribo Stim input_3


title: lib38399: Ribo Stim input_1


title: lib38405: Ribo Stim IP_2


title: lib38398: Ribo IL7 rest IP_5

value: IL7 rest


title: lib38396: Ribo IL7 rest IP_3


title: lib38395: Ribo IL7 rest IP_2


title: lib38394: Ribo IL7 rest IP_1


title: lib38397: Ribo IL7 rest IP_4


title: lib38393: Ribo IL7 rest input_5


title: lib38392: Ribo IL7 rest input_4


title: lib38404: Ribo Stim IP_1


title: lib38390: Ribo IL7 rest input_2


title: lib38389: Ribo IL7 rest input_1


title: lib38391: Ribo IL7 rest input_3


title: 29PAd4m2-4

status: Public on Jan 14 2022

description: 29PAd4m2-4 - lib55569

data_processing:
The processing workflow was managed on the Galaxy platform. Reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
Sequence alignment was performed using STAR aligner (v2.4.2a) with the GRCm38 reference genome and gene annotations from Ensembl release 91.
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134), FASTQC (v0.11.3), and HTSeq-count
Genome_build: GRCm38.91
Supplementary_files_format_and_content: The file "P393-1_RawGeneCounts.csv" is a comma-separated matrix. The first four columns ("geneId", "geneName", "description", and "geneBiotype") describe one gene per row, with the "geneId" column containing Ensembl gene IDs. The remaining columns are named as "sampleId - libraryId" and contain raw read counts assigned to each library. Counts have not been filtered or normalized.

source_name: lung

extract_protocol:
Total RNA was isolated using a NucleoSpin RNA midi kit (TaKaRa Clontech, Macherey-Nagel)
Reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.

treatment_protocol: MEK2-deficient and Wild-type mouse lungs have were collected for RNA at day 0 (naive), day 2 and day 4 post-infection with P. aeruginosa.

tag: agent

value: Pseudomona aeruginosa

tag: Sex

value: Male


title: 28PAd4m2-3

description: 28PAd4m2-3 - lib55568


title: 27PAd4m2-2

description: 27PAd4m2-2 - lib55567


title: 26PAd4m2-1

description: 26PAd4m2-1 - lib55566


title: 24PAd4wt4

description: 24PAd4wt4 - lib55564

value: WT


title: 23PAd4wt3

description: 23PAd4wt3 - lib55563


title: 22PAd4wt2

description: 22PAd4wt2 - lib55562


title: 25PAd4wt5

description: 25PAd4wt5 - lib55565


title: 20d0m2-5

description: 20d0m2-5 - lib55560

value: Female


title: lib38400: Ribo Stim input_2

value: spleen and lymph nodes

tag: stimulation

value: anti-CD3/CD28 beads


title: 21PAd4wt1

description: 21PAd4wt1 - lib55561

tag: timepoint


title: lib38402: Ribo Stim input_4

value: Input


title: 30PAd4m2-5

description: 30PAd4m2-5 - lib55570


title: 18d0m2-3

description: 18d0m2-3 - lib55558


title: 7PAd2m2-2

description: 7PAd2m2-2 - lib55547


title: 9PAd2m2-4

description: 9PAd2m2-4 - lib55549


title: 16d0m2-1

description: 16d0m2-1 - lib55556


title: 11d0wit1

description: 11d0wit1 - lib55551


title: 2PAd2wt2

description: 2PAd2wt2 - lib55542


title: 17d0m2-2

description: 17d0m2-2 - lib55557


title: 19d0m2-4

description: 19d0m2-4 - lib55559


title: 8PAd2m2-3

description: 8PAd2m2-3 - lib55548


title: 15d0wit5

description: 15d0wit5 - lib55555


title: 1PAd2wt1

description: 1PAd2wt1 - lib55541


title: 10PAd2m2-5

description: 10PAd2m2-5 - lib55550


title: 6PAd2m2-1

description: 6PAd2m2-1 - lib55546


title: 12d0wit2

description: 12d0wit2 - lib55552


title: 14d0wit4

description: 14d0wit4 - lib55554


title: 13d0wit3

description: 13d0wit3 - lib55553


title: 4PAd2wt4

description: 4PAd2wt4 - lib55544


title: Pig_002 Whole Liver Cells_Pig

status: Public on Jan 11 2022

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
Total RNA
Whole Liver Cells_Pig
Whole Liver Cells Pig_002
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq (version 3.1.0 or version 3.0.2)
Demultiplexed data was then processed using the Cell Ranger count pipeline (version 3.1.0 or version 3.0.2).
Cite-seq samples were mapped against the TotalSeqA whitelist.
Genome_build: mm10 (Mouse), hg19 (Human), GRCz10 (Zebrafish), MesAur1.0.100 (Hamster), GRCg6a.96 (Chicken), Sscrofa11.1.96 (Pig) or Macaca_facicularis_5.0.100 (Macaque)
Supplementary_files_format_and_content: h5 or txt files including raw gene – and if present – antibody counts (output CellRanger Count)
Supplementary_files_format_and_content: rds file: Seurat object

organism: Sus scrofa

source_name: Liver

extract_protocol: All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches. Cell. 2022.

tag: shortfilename

tag: platform

value: 10x Genomics – v3

tag: digestion method

value: Ex Vivo

tag: number of added abs

tag: number of cells


title: 5PAd2wt5

description: 5PAd2wt5 - lib55545


title: Zebrafish_001 Whole Liver Cells_Zebrafish

description:
Total RNA
Whole Liver Cells_Zebrafish
Whole Liver Cells Zebrafish_001

organism: Danio rerio

tag: strain


title: 3PAd2wt3

description: 3PAd2wt3 - lib55543

tag: genotype


title: Zebrafish_002 Liver mpeg1.1+ cells_Zebrafish

description:
Total RNA
Liver mpeg1.1+ cells_Zebrafish
Liver mpeg1.1+ cells Zebrafish_002


title: Zebrafish_002 Whole Liver Cells_Zebrafish

description:
Total RNA
Whole Liver Cells_Zebrafish
Whole Liver Cells Zebrafish_002


title: Macaque_001 Whole Liver Nuclei_Macaque

description:
Nuclear RNA
Whole Liver Nuclei_Macaque
Whole Liver Nuclei Macaque_001

organism: Macaca mulatta

value: Cynomolgus

value: 10x Genomics – v3.1

value: Nuclei


description:
Whole Liver_Visium+ADT_Mouse
Healthy Mouse Liver_ with Abs_Mouse_002_Sample_001

data_processing:
Raw sequencing data for each sample was converted to matrices of expression counts using the Space Ranger software provided by 10X Genomics (version 1.0).
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: h5 file including raw gene count (output Space Ranger) or txt file including raw antibody counts
Supplementary_files_format_and_content: json file including scale factors (output Space Ranger)
Supplementary_files_format_and_content: png file including tissue image (output Space Ranger)
Supplementary_files_format_and_content: csv file including tissue positions (output Space Ranger)
Supplementary_files_format_and_content: rds file: Seurat object

value: 10x Visium

tag: condition

value: StSt

tag: number of spots


title: Zebrafish_001 Liver mpeg1.1+ cells_Zebrafish

description:
Total RNA
Liver mpeg1.1+ cells_Zebrafish
Liver mpeg1.1+ cells Zebrafish_001


title: Pig_001 Whole Liver Cells_Pig

description:
Total RNA
Whole Liver Cells_Pig
Whole Liver Cells Pig_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Whole Liver_WD_36Wks_Visium_Mouse
Western diet fed (36 weeks) Mouse Liver_Mouse_002_Sample_002

value: WD


title: Macaque_002 Whole Liver Nuclei_Macaque

description:
Nuclear RNA
Whole Liver Nuclei_Macaque
Whole Liver Nuclei Macaque_002


description:
Whole Liver_WD_36Wks_Visium_Mouse
Western diet fed (36 weeks) Mouse Liver_Mouse_002_Sample_001


description:
Whole Liver_SD_36Wks_Visium_Mouse
Standard diet fed (36 weeks) Mouse Liver_Mouse_001_Sample_001

value: SD


description:
Whole Liver_Visium_Mouse
Healthy Mouse Liver_Mouse_001_Sample_002


description:
Nuclear RNA
Whole Liver Nuclei_WD_36wks_Mouse
Western diet fed (36 weeks) Liver nuclei_Mouse_003_Sample_001


description:
Whole Liver_WD_36Wks_Visium_Mouse
Western diet fed (36 weeks) Mouse Liver_Mouse_001_Sample_001


description:
Whole Liver_Visium_Mouse
Healthy Mouse Liver_Mouse_001_Sample_004


description:
Nuclear RNA
Whole Liver Nuclei_WD_36wks_Mouse
Western diet fed (36 weeks) Liver nuclei_Mouse_004_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_SD_36wks_Mouse
Standard diet fed (36 weeks) Liver nuclei_Mouse_003_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver nuclei_Mouse_007_Sample_001


description:
Total RNA
Liver_CD45- Cells_WD_36wks_Mouse
Western diet fed (36 weeks) Liver CD45- cells_Mouse_002_Sample_001

value: In Vivo


description:
Nuclear RNA
Whole Liver Nuclei_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver nuclei_Mouse_006_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_WD_24wks_Mouse
Western diet fed (24 weeks) Liver nuclei_Mouse_005_Sample_001


description:
Total RNA
Liver_CD45+ Cells_WD_36wks_Mouse
Western diet fed (236weeks) Liver CD45+ cells_Mouse_002_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_SD_36wks_Mouse
Standard diet fed (36 weeks) Liver nuclei_Mouse_004_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_WD_24wks_Mouse
Western diet fed (24 weeks) Liver nuclei_Mouse_006_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver nuclei_Mouse_008_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_WD_24wks_Mouse
Western diet fed (24 weeks) Liver nuclei_Mouse_008_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver nuclei_Mouse_005_Sample_001


description:
Total RNA
Whole Liver Cells_Mouse
Healthy Mouse Liver_Stained with human Abs_Mouse_003_Sample_001


description:
Total RNA
Liver_Capsule_CD45+ Cells_Mouse
Healthy Mouse Liver Capsule CD45+ Cells_Mouse_005_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_SD_36wks_Mouse
Standard diet fed (36 weeks) Liver CD45- cells_Mouse_002_Sample_001


description:
Total RNA
Liver_Hepatocytes_Mouse
Healthy Mouse Liver Hepatocytes_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_SD_36wks_Mouse
Standard diet fed (36 weeks) Liver CD45+ cells_Mouse_002_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_WD_24wks_Mouse
Western diet fed (24 weeks) Liver nuclei_Mouse_004_Sample_001


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_004_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Whole Liver_Visium_Mouse
Healthy Mouse Liver_Mouse_001_Sample_003


description:
Liver Capsule_Visium_Mouse
Healthy Mouse Liver Capsule_Mouse_002_Sample_001


description:
Whole Liver_Visium_Mouse
Healthy Mouse Liver_Mouse_001_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_WD_24wks_Mouse
Western diet fed (24 weeks) Liver nuclei_Mouse_007_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver nuclei_Mouse_004_Sample_001


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_003_Sample_002
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_004_Sample_004


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_004_Sample_003


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_004_Sample_002


description:
Nuclear RNA
Liver Capsule Nuclei_Mouse
Healthy Mouse Liver Capsule Nuclei_Mouse_001_Sample_001


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Pre-stained_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_001_Sample_003


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_001_Sample_001


description:
Total RNA
Liver_CD45+ Cells_WD_24wks_Mouse
Western diet fed (24 weeks) Liver CD45+ cells_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_WD_24wks_Mouse
Western diet fed (24 weeks) Liver CD45- cells_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_003_Sample_002


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_003_Sample_002
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_WD_36wks_Mouse
Western diet fed (36weeks) Liver CD45+ cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver CD45- cells_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_SD_36wks_Mouse
Standard diet fed (36 weeks) Liver CD45+ cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_002_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_001_Sample_002


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_002_Sample_002


description:
Total RNA
Liver_DCs_WD_24wks_Mouse
Western diet fed (24 weeks) Liver DCs_Mouse_002_Sample_001

value: 10x Genomics – v2


description:
Total RNA
Liver_CD45+ Cells_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver CD45+ cells_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_SD_36wks_Mouse
Standard diet fed (36 weeks) Liver CD45- cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_monos+macs_WD_24wks_Mouse
Western diet fed (24 weeks) Liver monos+macss_Mouse_002_Sample_001


description:
Total RNA
Liver_DCs_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver DCs_Mouse_002_Sample_001


description:
Total RNA
Liver_monos+macs_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver monos+macs_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Pre-stained_Mouse_003_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_WD_24wks_Mouse
Western diet fed (24 weeks) Liver CD45- cells_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45+ Cells_WD_24wks_Mouse
Western diet fed (24 weeks) Liver CD45+ cells_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45+ Cells_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver CD45+ cells_Mouse_002_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_004_Sample_001


description:
Nuclear RNA
Whole Liver Nuclei_Mouse
Healthy Mouse Liver Nuclei_Mouse_003_Sample_001


description:
Total RNA
Liver_CD45- Cells_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver CD45- cells_Mouse_002_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_Myeloid Cells_SD_24wks_Mouse
Standard diet fed (24 weeks) Liver Myeloid cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_002_Sample_003


description:
Total RNA
Liver_CD45- Cells_WD_36wks_Mouse
Western diet fed (36 weeks) Liver CD45- cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_Myeloid Cells_WD_24wks_Mouse
Western diet fed (24 weeks) Liver Myeloid cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_002_Sample_003


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_002_Sample_002
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_001_Sample_002
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_002_Sample_002


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_001_Sample_002


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_001_Sample_003


description:
Total RNA
Liver_CD45+ Cells_PBS-Fed_Mouse
PBS Oral Gavage, 24hours, Liver CD45+ cells_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45+ Cells_Mouse
Healthy Mouse Liver CD45+ Cells_Mouse_001_Sample_001


description:
Total RNA
Liver_CD45- Cells_PBS-Fed_Mouse
PBS Oral Gavage, 24hours, Liver CD45- cells_Mouse_002_Sample_001


description:
Total RNA
Liver_Hepatocytes_PBS-Fed_Mouse
PBS Oral Gavage, 24hours, Liver Hepatocytes_Mouse_002_Sample_001


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_001_Sample_001


description:
Total RNA
Liver_CD45+ Lineage- Cells_PBS-Fed_Mouse
PBS Oral Gavage, 24hours, Liver CD45+ Lineage-  cells_Mouse_002_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver CD45+ cells_Mouse_002_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_DCs_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver DCs_Mouse_003_Sample_001


description:
Total RNA
Liver_Myeloid Cells_PBS-Fed_Mouse
PBS Oral Gavage, 24hours, Liver Myeloid cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver CD45- cells_Mouse_002_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_PBS-Fed_Mouse
PBS Oral Gavage, 24hours, Liver CD45+ cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver CD45+ cells_Mouse_001_Sample_003
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver CD45+ cells_Mouse_001_Sample_002
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45- Cells_ Human H25

description:
Total RNA
Liver_CD45- Cells_ Human
Liver_CD45- Cells_ Human H25


description:
Total RNA
Liver_CD45+ Cells_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver CD45+ cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_Myeloid Cells_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver Myeloid cells_Mouse_001_Sample_001
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45- Cells_Mouse
Healthy Mouse Liver CD45- Cells_Mouse_001_Sample_003


title: Liver_CD45+ Cells_ Human H25

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H25


title: Liver_CD45+ Cells_ Human H23

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H23


title: Liver_CD45- Cells_ Human H22

description:
Total RNA
Liver_CD45- Cells_ Human
Liver_CD45- Cells_ Human H22


title: Liver_CD45+ CD14+CD16+ Cells_ Human H21

description:
Total RNA
Liver_CD45+ CD14+CD16+ Cells_ Human
Liver_CD45+ CD14+CD16+ Cells_ Human H21


title: Liver_CD45+ Cells_ Human H18

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H18
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45+ Cells_ Human H16 (sample2)

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H16
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45+ Cells_ Human H16 (sample1)

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H16


description:
Total RNA
Liver_monos+macs_SD_12wks_Mouse
Standard diet fed (12 weeks) Liver monos+macs_Mouse_003_Sample_001


title: Liver_CD45+ Cells_ Human H10

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H10


title: Liver_CD45+ Cells_ Human H11

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H11
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45+ Cells_ Human H21

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H21


title: iver_CD45+ Cells_ Human H07

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H07


title: Liver_CD45+ Cells_ Human H06 (sample2)

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H06


title: Liver_CD45+ Cells_ Human H13

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H13
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45+ Cells_ Human H06 (sample3)

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H06
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45+ Cells_ Human H06 (sample1)


title: Liver_CD45+ Cells_ Human H06 (sample4)


title: Liver CD45- Cells_Human H02

description:
Total RNA
Liver CD45- Cells_Human
Liver CD45- Cells_Human H02


title: Liver_DCs_Human H02 (sample1)

description:
Total RNA
Liver_DCs_Human
Liver_DCs_Human H02


description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H02 Abs at 1:30 or 1:200
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Liver_CD45+ Cells_ Human H04 (sample1)

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H04


title: Liver_monos+macs_Human H02

description:
Total RNA
Liver_monos+macs_Human
Liver_monos+macs_Human H02


title: Liver_DCs_Human H02 (sample2)


title: Liver_CD45+ Cells_ Human H22

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H22


description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H02 Abs at 1:200
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Hamster_002 Whole Liver Cells_Hamster

description:
Total RNA
Whole Liver Cells_Hamster
Whole Liver Cells Hamster_002

organism: Mesocricetus auratus

value: Syrian


title: Hamster_001 Whole Liver Cells_Hamster

description:
Total RNA
Whole Liver Cells_Hamster
Whole Liver Cells Hamster_001


title: Chicken_002 Whole Liver Cells_Chicken

description:
Total RNA
Whole Liver Cells_Chicken
Whole Liver Cells Chicken_002

organism: Gallus gallus

value: Leghorn


description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H02 Abs at 1:500
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H02 Abs at 1:30
NOTE: adt-CLEC4F and adt-VSIG4 are custom Abs and their names got swapped in the CellRanger output.
To get the expression of adt-VSIG4, you need to look at adt-CLEC4F. To see the expression of adt-CLEC4F, please look at adt-VSIG4.


title: Chicken_001 Whole Liver Cells_Chicken

description:
Total RNA
Whole Liver Cells_Chicken
Whole Liver Cells Chicken_001


title: Liver_CD45+ Cells_ Human H14

description:
Total RNA
Liver_CD45+ Cells_ Human
Liver_CD45+ Cells_ Human H14


title: Whole Liver_Visium of Human H35 (sample2)

description:
Whole Liver_Visium_Human
Whole Liver_Visium of H35

value: Steatotic


title: Whole Liver Nuclei_Human H38 (sample1)

description:
Nuclear RNA
Whole Liver Nuclei_Human
Whole Liver Nuclei_Human H38


title: Liver_CD45+ Cells_ Human H04 (sample2)


title: Whole Liver_Visium of Human H35 (sample1)


title: Whole Liver_Visium of Human H38

description:
Whole Liver_Visium_Human
Whole Liver_Visium of H38

value: Healthy


title: Whole Liver Nuclei_Human H32

description:
Nuclear RNA
Whole Liver Nuclei_Human
Whole Liver Nuclei_Human H32


title: Whole Liver_Visium of Human H37

description:
Whole Liver_Visium_Human
Whole Liver_Visium of H37


title: Whole Liver Nuclei_Human H38 (sample2)

description:
Total RNA
Whole Liver Nuclei_Human
Whole Liver Nuclei_Human H38


title: Whole Liver Nuclei_Human H37 (sample3)

description:
Nuclear RNA
Whole Liver Nuclei_Human
Whole Liver Nuclei_Human H37


title: Whole Liver Nuclei_Human H37 (sample2)


title: Whole Liver Nuclei_Human  H33

description:
Nuclear RNA
Whole Liver Nuclei_Human
Whole Liver Nuclei_Human  H33


title: Whole Liver Nuclei_Human H30 (sample2)

description:
Nuclear RNA
Whole Liver Nuclei_Human
Whole Liver Nuclei_Human H30


title: Whole Liver_Visium of Human H36

description:
Whole Liver_Visium_Human
Whole Liver_Visium of H36


title: Whole Liver Nuclei_Human H37 (sample1)


title: Whole Liver Nuclei_Human H30 (sample1)


title: 8.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-

status: Public on Dec 22 2021

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned by STAR1 2.4.2a to GRCm38.91
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCm38.91
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: colon

growth_protocol: Seven to twelve-week-old BALB/c mice, Foxp3IRES-cre mice and Foxp3YFP-cre mice were purchased from Jackson Laboratory.  Tslp-/-, Il1rl1-/- and Tslpr-/-Il1rl1-/- mice are backcrossed to BALB/c background for more than 10 generations (42, 43).  Mice with conditional TSLPR alleles were on BALB/c for crossing with Foxp3IRES-cre mice.  Age and sex matched mice were used for controls.  All animals were bred and housed in specific-pathogen free conditions in Benaroya Research Institute animal facility.

extract_protocol:
Colon tissue was cut into small pieces and treated with 2 mM EDTA, followed by digestion with collagenase D (50 μg/mL) (Sigma-Aldrich) and DNase (20 units/mL) (Sigma-Aldrich) in HEPES buffer for 30 min.  Cells were filtrated through a 100μm filter to make single cell suspensions, subjected to staining with fluorescent-labeled antibodies for flow cytometry. T cell subsets were sorted on a BD FACSAria II cell sorter (BD Biosciences).  Cell subsets (200 cells per sample) were sorted directly into SMART-Seq v4 lysis buffer (Takara Bio) to release RNA.
Reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.  Sequencing libraries were constructed using a modified protocol of the Nextera XT DNA Sample Preparation Kit (Illumina) to generate Illumina-compatible barcoded libraries
Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq 2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS Kits (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: For colitis-associated cancer model mice received one intraperitoneal (i.p.) injection of Azoxymethane (AOM; 10 mg/kg) on day 0, followed by administration of the indicated dose of Dextran Sodium Sulfate (DSS; 36,000-50,000 M.Wt.) in their drinking water for 7 days after AOM treatment. This treatment was followed by administration of regular drinking water for two weeks.  One week of DSS and two weeks in regular drinking water constitute 1 full cycle of DSS.  Mice were given two full cycles of DSS after the AOM injection for BALB/c background mice, three full cycles of DSS for C57BL/6 background mice.  Mice were euthanized 2 weeks after final treatment of DSS.

tag: cancer status

value: cancer

tag: sort

value: Foxp3-yfp B6


title: 8.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: 8.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: 38W-1

status: Public on Jan 10 2022

type: RNA

city: Houston

first: Kalluri

last: Lab

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using GenomeStudio

source_name: Mouse skin

label_protocol: Standard Illumina protocol

extract_protocol: RNA (500ng) was isolated using Trizol Reagent and quality controlled by BioAnalyzer

tag: time

value: Day 17

value: WT


title: 22W-1


title: TK-37-3

value: aSMA-TK


title: 22W-2


title: 320a

value: Day 6


title: p35b


title: TK-7-2


title: p35a


title: 38W-3


title: 320b


title: p36b


title: p36a


title: TK-37-2


title: 38W-2


title: TK-37-1


title: 8.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 22W-3


title: TK-7-3


title: p34b


title: 319b


title: 7.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 7.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: p34a


title: 7.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 6.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: 7.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: 6.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 316a


title: 5.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 6.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 5.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: TK-7-1


title: 5.cancer.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: Tn.naive.CD45+TCR+CD4+Fox+3-CD44low

value: naive

value: Tn


title: 4.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 4.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: 316b


title: 3.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 3.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 319a


title: 2.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 4.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 3.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: 2.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: 1.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1-


title: 6.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: 2.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 1.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: 3.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: 1.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1-


title: 5.cancer.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 1.naive.CD45+TCR+CD4+Fox+3+TSLPR-Il1rl1+


title: 4.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: 2.naive.CD45+TCR+CD4+Fox+3+TSLPR+Il1rl1+


title: CRISPRi LTR10 MEF2D rep2

status: Public on Oct 31 2021

city: Boulder

first: Edward

middle: Boyi

last: Chuong

state: CO

address: JSC Biotech Building, 3415 Colorado Ave

department: BioFrontiers Institute and Molecular, Cellular & Developmental Biology Department

institute: University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 with arguments 'ktrim=r k=31 mink=11 hdist=1 qtrim=r trimq=10 tpe tbo' and mapped to hg38 using hisat2 v2.1.0 with options '--rna-strandness RF --no-softclip'. Aligned fragments with an alignment score less than 10 were removed with samtools v1.10. Samples were mapped to Gencode genes in the GENCODE v34 annotation using featureCounts v1.6.2 with options '-s 2 -t exon -g gene_id -0 -p'. For visualization, aligned fragments were converted to stranded, CPM normalized bigwigs using deepTools bamCoverage v3.0.1.
Differentially expressed genes were called using DESeq2 v1.32.0 with design '~ condition'. For the CRISPR-KO differential expression analysis, normalized count data is derived from DESeq2 comparisons between the KO (3 replicates) vs untreated HCT116 samples (2 replicates). For the CRISPRi differential expression analysis, GFP (2 replicates) were used as the control. Genes with zero counts across all samples were removed.
Genome_build: hg38
Supplementary_files_format_and_content: CPM normalized signal tracks in UCSC bigwig format
Supplementary_files_format_and_content: Tab-delimited text files including DESeq2 normalized counts

molecule: polyA RNA

source_name: Colorectal cancer cell line

growth_protocol: HCT116 cells were routinely grown at 37C in 5% CO2 on coated plastic (VWR #10861-680, typically 1,000,000-2,000,000 cells in 10cm dishes) in McCoy’s 5A (Gibco #16600082) supplemented with 1X penicillin-streptomycin (Gibco #15140122), and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
RNA from HCT116 was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1057).
Libraries were generated with 500 ng RNA using KAPA mRNA HyperPrep Kit (KAPA #KK8581) according to the manufacturer's instructions. Briefly, single-indexed adapters (KAPA #KK8700) or unique dual-indexed adapters (KAPA #KK8727) were added to each sample at a final concentration of 78 nM. Excess adapter was removed using sequential 0.63X and 0.70X KAPA Pure Bead (KAPA #KK8002) cleanups. Purified, adapter-ligated samples were amplified for 11 cycles according to the manufacturer's instructions and purified using a 1.0X KAPA Pure Bead cleanup.

treatment_protocol: HCT116 cells were either untreated or treated with 1 uM Cobimteinib or 100 ng/mL TNF-alpha for 24h. For the HCT116 cell line-based xenografts, HCT116 cells were engrafted into two immunodeficient mice, which were dosed at 0.125 mg/kg trametinib or vehicle by oral gavage daily for 21 days.

tag: cell line

tag: treatment

value: untreated


title: CRISPRKO LTR10 KDM6A rep3

value: Cas9_CRISPRKO_LTR10.KDM6A -/-


title: CRISPRKO LTR10 KDM6A rep2


title: CRISPRi LTR10 MCPH1 rep2


title: CRISPRi LTR10 MEF2D rep1


title: CRISPRi LTR10 XRCC4 rep2


title: CRISPRi LTR10 MCPH1 rep1


title: CRISPRi LTR10 XRCC4 rep1


title: CRISPRKO LTR10 KDM6A rep1


title: CRISPRi LTR10 ATG12 rep2


title: CRISPRi LTR10 FGF2 rep1


title: CRISPRi LTR10 ATG12 rep1


title: CRISPRi FOSL rep2

value: dCas9_CRISPRi_FOSL (TSS)


title: CRISPRi FOSL rep1


title: CRISPRi LTR10 FGF2 rep2


title: CRISPRi cJun rep2

value: dCas9_CRISPRi_cJun (TSS)


title: CRISPRi cJun rep1


title: CRISPRi ATG12 rep2

value: dCas9_CRISPRi_ATG12 (TSS)


title: CRISPRi ATG12 rep1


title: healthy control 4 rep

status: Public on Dec 12 2021

city: Beijing

first: Xiaohan

last: Fan

address: Beilishi Road 167

country: China

institute: Fuwai Hospital

hyb_protocol: Array hybridization and wash were performed using GeneChip Hybridization, Wash and Stain Kit (Affymetrix) in Hybridization Oven 645 (Affymetrix) and Fluidics Station (Affymetrix) by following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip Scanner 3000 (Affymetrix) and Command Console Software 3.1 (Affymetrix) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: biotin

source_name: aortic tissues

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Aortic tissues obtained from patients with aortic dissection and the healthy controls were stored in liquid nitrogen for RNA extraction.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Aortic tissues obtained in liquid nitrogen were grinded to a fine powder in liquid nitrogen.

tag: tissue

value: aorta tissue

tag: disease state

value: healthy control


title: healthy control 3 rep


title: CRISPRi GFP rep1

tag: timepoint


title: TNFalpha 24hr rep2

value: wildtype

value: TNFalpha


title: TNFalpha 24hr rep1


title: Cobimetinib 24hr rep2

value: Cobimetinib


title: Untreated rep1


title: lib55125

status: Public on Sep 11 2021

description:
lib55125_AAAHMLVM5
81_rn1046833680

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the STAR aligner with the GRCh38 reference genome
Gene counts were generated using HTSeq-count (v0.4.1)29. Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38 reference genome and gene annotations from ensembl release 77
Supplementary_files_format_and_content: Processed data is in .csv format. Each row is a gene, each column is a sample.

source_name: Whole Blood

growth_protocol: Whole blood was collected in Tempus tubes (Ambion).

extract_protocol:
Total RNA was isolated from whole blood samples using MagMax for Stabilized Blood Tubes RNA Isolation Kit (Ambion) and globin-reduced using GLOBINclear (Ambion) per manufacturer's instructions.
Globin-reduced RNA was used to construct libraries using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), with reverse transcription followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.
Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).  Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 53-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample.

tag: registry

value: Type 1 Diabetes

tag: age at draw

tag: Sex

value: female

value: Whole Blood


title: Untreated rep2


title: lib55124

description:
lib55124_AAAHMLVM5
80_rn722743960

value: male


title: lib55123

description:
lib55123_AAAHMLVM5
79_rn591717547


title: aortic dissection patient 4 rep

value: patient with aortic dissection


title: lib55121

description:
lib55121_AAAHMLVM5
77_rn968172181

value: Control


title: lib55122

description:
lib55122_AAAHMLVM5
78_rn388837636


title: lib55118

description:
lib55118_AAAHMLVM5
74_rn1062948954


title: healthy control 1 rep


title: lib55120

description:
lib55120_AAAHMLVM5
76_rn875124480


title: healthy control 2 rep


title: lib55119

description:
lib55119_AAAHMLVM5
75_rn1066748273


title: CRISPRi GFP rep2


title: lib55117

description:
lib55117_AAAHMLVM5
73_rn999769413

value: DSRegistry


title: lib55113

description:
lib55113_AAAHMLVM5
69_rn904394254


title: lib55116

description:
lib55116_AAAHMLVM5
72_rn443736542


title: lib55114

description:
lib55114_AAAHMLVM5
70_rn750172559


title: lib55112

description:
lib55112_AAAHMLVM5
68_rn568848184


title: lib55110

description:
lib55110_AAAHMLVM5
66_rn118797159


title: lib55109

description:
lib55109_AAAHMLVM5
65_rn706609037


title: lib55111

description:
lib55111_AAAHMLVM5
67_rn280693905


title: Cobimetinib 24hr rep1


title: lib55108

description:
lib55108_AAAHMLVM5
64_rn337702217


title: lib55107

description:
lib55107_AAAHMLVM5
63_rn284981205


title: lib55106

description:
lib55106_AAAHMLVM5
62_rn562124807


title: lib55115

description:
lib55115_AAAHMLVM5
71_rn555402675


title: lib55103

description:
lib55103_AAAHMLVM5
59_rn902445994


title: lib55100

description:
lib55100_AAAHMLVM5
56_rn249066991


title: lib55104

description:
lib55104_AAAHMLVM5
60_rn588789064


title: lib55102

description:
lib55102_AAAHMLVM5
58_rn853593638


title: lib55101

description:
lib55101_AAAHMLVM5
57_rn227911792


title: lib55105

description:
lib55105_AAAHMLVM5
61_rn821315683


title: lib55095

description:
lib55095_AAAHMLVM5
51_rn812568043


title: lib55099

description:
lib55099_AAAHMLVM5
55_rn975565578


title: lib55096

description:
lib55096_AAAHMLVM5
52_rn1034968531


title: lib55097

description:
lib55097_AAAHMLVM5
53_rn401506490


title: lib55094

description:
lib55094_AAAHMLVM5
50_rn337947651


title: lib55093

description:
lib55093_AAAHMLVM5
49_rn723509272


title: aortic dissection patient 2 rep


title: lib55098

description:
lib55098_AAAHMLVM5
54_rn984581603


title: lib55092

description:
lib55092_AAAHMLVM5
48_rn1084493241


title: lib55087

description:
lib55087_AAAHMLVM5
42_rn797010866


title: lib55090

description:
lib55090_AAAHMLVM5
46_rn746728292


title: lib55086

description:
lib55086_AAAHMLVM5
41_rn875813340


title: lib55084

description:
lib55084_AAAHMLVM5
39_rn387024146


title: lib55091

description:
lib55091_AAAHMLVM5
47_rn423028985


title: aortic dissection patient 3 rep


title: aortic dissection patient 1 rep


title: lib55082

description:
lib55082_AAAHMLVM5
36_rn911806702


title: lib55089

description:
lib55089_AAAHMLVM5
44_rn558032091


title: lib55083

description:
lib55083_AAAHMLVM5
38_rn708308783


title: lib55081

description:
lib55081_AAAHMLVM5
35_rn1078250554


title: lib55080

description:
lib55080_AAAHMLVM5
34_rn1014516837


title: lib55077

description:
lib55077_AAAHMLVM5
31_rn423285741


title: lib55073

description:
lib55073_AAAHMLVM5
26_rn521560381


title: lib55074

description:
lib55074_AAAHMLVM5
27_rn941335766


title: lib55075

description:
lib55075_AAAHMLVM5
28_rn497329890


title: lib55076

description:
lib55076_AAAHMLVM5
30_rn923993791


title: lib55072

description:
lib55072_AAAHMLVM5
25_rn257367547


title: lib55070

description:
lib55070_AAAHMLVM5
23_rn544461960


title: lib55078

description:
lib55078_AAAHMLVM5
32_rn226917827


title: lib55066

description:
lib55066_AAAHMLVM5
18_rn142097657


title: lib55065

description:
lib55065_AAAHMLVM5
16_rn200189330


title: lib55068

description:
lib55068_AAAHMLVM5
20_rn998408054


title: lib55079

description:
lib55079_AAAHMLVM5
33_rn641102437


title: lib55063

description:
lib55063_AAAHMLVM5
14_rn894249852


title: lib55067

description:
lib55067_AAAHMLVM5
19_rn241387619


title: lib55062

description:
lib55062_AAAHMLVM5
13_rn327434448


title: lib55064

description:
lib55064_AAAHMLVM5
15_rn243781973


title: lib55085

description:
lib55085_AAAHMLVM5
40_rn592867185


title: lib55061

description:
lib55061_AAAHMLVM5
12_rn283015536


title: lib55060

description:
lib55060_AAAHMLVM5
11_rn203402604


title: lib55058

description:
lib55058_AAAHMLVM5
9_rn966003677


title: lib55057

description:
lib55057_AAAHMLVM5
8_rn875164645


title: lib55071

description:
lib55071_AAAHMLVM5
24_rn1070417950


title: lib55055

description:
lib55055_AAAHMLVM5
6_rn500538064


title: lib55059

description:
lib55059_AAAHMLVM5
10_rn699477612


title: lib55056

description:
lib55056_AAAHMLVM5
7_rn977253701


title: lib55053

description:
lib55053_AAAHMLVM5
4_rn919632875


title: lib55054

description:
lib55054_AAAHMLVM5
5_rn971141720


title: lib55052

description:
lib55052_AAAHMLVM5
3_rn426194021


title: lib55051

description:
lib55051_AAAHMLVM5
2_rn946260263


title: Lens Epithelium from Female Young Mice, 24 Hours post surgery, rep 2

status: Public on Jul 10 2021

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

department: Biological Sciences

institute: University of Delaware

description:
Y_24_hr_4F_S64
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx

data_processing:
Reads were trimmed for quality, adaptor content, and to remove a kit specific trinucleotide sequence using the software "TrimGalore!" with the following parameters: --length 85 --paired --clip_R2 3 --phred33
Trimmed reads were aligned using Hisat2 with the following parameters: -p8 --verbose --dta --fr --phred33
Aligned reads were sorted by position using samtools sort.
Aligned reads were quantified using Htseq-Count with the following parameters: -i gene_id -r pos -f bam -s reverse -m union --type exon
Gene level counts were analyzed for differential expression using the edgeR.
Genome_build: GRCm38, GTF File: Mouse Ensembl version 101
Supplementary_files_format_and_content: *_GeneCount.txt: Htseq-count, Tab Separated, Column 1: Ensembl Gene ID, Column 2: Count.

source_name: LEC

extract_protocol:
Lens epithelial cell RNA was harvested using the RNeasy Mini Kit (50) from Qiagen (Cat No./ID: 74104), and lens fiber cell RNA isolated using the SV Total RNA Isolation System (Promega- Catalog number- Z3100).
SMARTer® Stranded Total RNA-Seq Kit-Pico Input Mammalian v2 (Takara Bio USA, Inc., Mountain View, CA, USA).
Paired end 100 nucleotide reads, ribosomal depletion.

tag: cell type

value: Lens epithelial cells (LEC)

tag: age

value: 3 Months

value: Female


title: Lens Fibers from Male Young Mice, 0 Hours post surgery, rep 1

description:
YF_1M_S73
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx

source_name: LFC

value: Lens fiber cells (LFC)

value: Male


title: Lens Fibers from Female Young Mice, 0 Hours post surgery, rep 2

description:
YF_4F_S76
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: lib55069

description:
lib55069_AAAHMLVM5
22_rn1097949475


title: lib55050

description:
lib55050_AAAHMLVM5
1_rn694638471


title: Lens Fibers from Male Young Mice, 0 Hours post surgery, rep 2

description:
YF_2M_S74
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Fibers from Female Young Mice, 0 Hours post surgery, rep 1

description:
YF_3F_S75
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Young Mice, 0 Hours post surgery, rep 1

description:
Y_0_hr_3F_S59
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Young Mice, 24 Hours post surgery, rep 1

description:
Y_24_hr_1M_S61
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Young Mice, 24 Hours post surgery, rep 1

description:
Y_24_hr_3F_S63
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Young Mice, 0 Hours post surgery, rep 2

description:
Y_0_hr_2M_S58
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Young Mice, 24 Hours post surgery, rep 2

description:
Y_24_hr_2M_S62
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_YE24vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Young Mice, 0 Hours post surgery, rep 2

description:
Y_0_hr_4F_S60
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Young Mice, 0 Hours post surgery, rep 1

description:
Y_0_hr_1M_S57
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_YF0vYE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Fibers from Female Aged Mice, 0 Hours post surgery, rep 2

description:
AF_4F_S80
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx

value: 24 Months


title: Lens Fibers from Female Aged Mice, 0 Hours post surgery, rep 1

description:
AF_3F_S79
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Fibers from Male Aged Mice, 0 Hours post surgery, rep 1

description:
AF_1M_S77
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Fibers from Male Aged Mice, 0 Hours post surgery, rep 2

description:
AF_2M_S78
All0H_AF0vYF0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Aged Mice, 24 Hours post surgery, rep 1

description:
A_24_hr_3F_S71
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Aged Mice, 0 Hours post surgery, rep 2

description:
A_0_hr_4F_S68
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Aged Mice, 0 Hours post surgery, rep 1

description:
A_0_hr_1M_S65
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Aged Mice, 24 Hours post surgery, rep 2

description:
A_24_hr_2M_S70
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Male Aged Mice, 0 Hours post surgery, rep 2

description:
A_0_hr_2M_S66
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Aged Mice, 24 Hours post surgery, rep 2

description:
A_24_hr_4F_S72
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: Lens Epithelium from Female Aged Mice, 0 Hours post surgery, rep 1

description:
A_0_hr_3F_S67
All0H_AE0vYE0_ExactTestQVL_Differential_Expression.xlsx
All0H_AF0vAE0_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: mkpto_old rep 3

status: Public on Jun 01 2021

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

institute: Institute for the Biology of Stem Cells, University of California Santa Cruz

data_processing:
Paired-end Illumina reads were trimmed to 75x75bp.
Bowtie2 was used to filter reads for the mouse genome.
STAR was used to map to mm10 assembly
DESeq  was used to perform differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: DESeq results for genes analyzed comparing the mkpy replicates to the mkpo replicates.

source_name: Bone marrow, 18-20 month

growth_protocol: Flt3-cre mice were crossed to mTmG mice and offspring were aged to 3 months (young) or 20 months old (old)

extract_protocol:
Total RNA was isolated from sorted  using trizol and following manufacturers instructions
RNA-seq libraries  were prepared using NEBNext® Ultra kit (New England Biolabs, using Tn5) following manufacturer instructions

treatment_protocol: Bone Marrow cells were stained with fluorescent antibodies, and Tom+ or GFP+ fractions of Lin-cKit+Sca1-CD150+CD41+ cells were isolated by flow cytometry

tag: strain

value: Megakaryocyte Progenitor

value: old


title: mkpto_old rep 4


title: mkpgo_old rep 1


title: mkpgo_old rep 2


title: mkpgy_young rep 3

source_name: Bone marrow, 3 month

value: young


title: mkpgy_young rep 2


title: genomic DNA from buccal swab 541 [201557560057_R05C01]

status: Public on Feb 19 2021

type: genomic

city: Atlanta

first: Carmen

last: Marsit

state: GA

address: 1518 Clifton Road

department: Environmental Health

institute: Rollins School of Public Health at Emory University

description: human buccal swab

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Control Software using standard recommended Illumina scanner setting

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. Normalization was performed using the Functional Normalization function implemented in minfi

label: Cy5 and Cy3

source_name: genomic DNA from buccal swab

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from buccal swab samples, collected near term-equivalent age, using the Isohelix Buccal Swab system (Boca Scientific), quantified using the Quibit Fluorometer (Thermo Fisher, Waltham, MA, USA) and aliquoted into a standardized concentration for subsequent analyses

tag: gender

tag: class

value: Typical

tag: rid

tag: rfid

tag: epi


title: mkpgy_young rep 1


title: genomic DNA from buccal swab 542 [201557550031_R08C01]

description: human buccal swab

tag: baycogcb

tag: bayccogcb


title: SC cells-enhancer-4C-seq

status: Public on Mar 03 2021

city: Tianjin

first: Mulin Jun

last: Li

state: Tianjin

address: No.22, Qixiangtai Road, Hepin

department: Basic Medical Research Center

institute: Tianjin Medical University

data_processing:
All libraries were sequenced using an Illumina Novaseq sequencer and 150 bp paired-end format.
4C-seq reads were aligned to the hg19 genome assembly using bwa version 0.7.13 with "mem -t 10".
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for 4C-seq were generated by Basic4Cseq

source_name: SC cells

extract_protocol:
For RNA-seq, RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
For ATAC-seq, ATAC-seq assay was performed as previously described (Corces et al., 2017) with modifications. Briefly, SC cells were pretreated with DNase I (Worthington, LS002007) to digest DNA from dead cells and to remove free-floating DNA. The cells were counted with Crystal Violet (Sigma-Aldrich, C0775), and ~50,000 cells (for each sample) were resuspended in 1 ml cold ATAC-Resuspension Buffer (RSB; 3 mM MgCl2 [Sigma-Aldrich, M2670], 10 mM Tris-HCl pH 7.5 [ThermoFisher, 15567027], and 10 mM NaCl [Sigma-Aldrich, S7653] in sterile H2O). After centrifugation, the supernatant was discarded, and the cell pellets were resuspended in 50 μl cold RSB containing 0.1% Tween-20 (Sigma-Aldrich, P1379), 0.1% NP-40 (ThermoFisher, FNN0021) and 0.01% Digitonin (Sigma-Aldrich, D141). After lysis, 1 ml RSB containing 0.1% Tween-20 was added, and the tube was inverted several times to mix. After centrifugation, the supernatant was removed, and the nuclei were resuspended in 50 μl Transposition Mix (Vazyme, TD501). Then, the transposition reaction was incubated at 37°C for 25 min with shaking at 1,000 rpm. The reaction products were purified with the QIAquick PCR Purification Kit (QIAGEN, 28106). The ATAC-seq library was prepared using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) and TruePrep Index Kit V2 for Illumina (Vazyme, TD202) according to the manufacturer’s instructions. The ATAC-seq analysis sequences with adaptor and low quality were trimmed for all 150-bp pair-end ATAC-seq reads. The clean reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 (v2.2.1) (Langmead and Salzberg, 2012) in the default parameters. All the samples were separately processed, and duplicate reads were removed. The ATAC-seq peak regions of each sample were called using MACS2 (v2.1.1) (Zhang et al., 2008) in the default parameters. The results were analyzed and visualized in IGV (v2.8.6) (Thorvaldsdottir et al., 2013). For ChIP-seq, ChIP assays were performed as previously described (Li et al., 2017c) with modifications. Briefly, for each sample, ~1 × 107 SC cells were cross-linked with 1% formaldehyde (Sigma-Aldrich, F8775) in 10% FBS/phosphate-buffered saline (PBS) for 10 min at room temperature and quenched with 0.125 M glycine (Sigma-Aldrich, 50046). The cells were then collected and lysed twice with ice-cold lysis buffer (20 mM Tris-HCl pH 7.5 [ThermoFisher, 15567027], 2 mM EDTA [ThermoFisher, 15575020], 1% Triton X-100 [Sigma-Aldrich, T8787], 0.1% SDS [ThermoFisher, 15525017], 0.1% Sodium Deoxycholate [Sigma-Aldrich, D6750], and 1× Protease Inhibitors [ThermoFisher, 78425]) for 10 min with slow rotations at 4 °C. The nuclear lysates were sonicated to obtain DNA fragments of 200~500 bp using a Biorupter system (Diagenode, B01060001) by high energy, with a working time of 30 s and a resting time of 30 s, 30 cycles, until the solutions turned clear. After removing insoluble debris, the lysates were separately incubated with specific antibodies against Rabbit IgG (CST, 7074), ZBTB3 (Novus Biologicals, NBP1-82079), CTCF (Abcam, ab128873), RAD21 (Abcam, ab992), H3K4me1 (CST, 5326), H3K4me3 (CST, 9751), or H3K27ac (Abcam, ab4729), and then purified by protein A-agarose beads (Millipore, 16-157). The beads were washed 4 times by TE buffer (10 mM Tris-HCl pH 8.0 [ThermoFisher, 15568025], and 1 mM EDTA), TSE I buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), TSE II buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), and Buffer III (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 0.25 M LiCl [Sigma-Aldrich, L4408], and 1% Sodium Deoxycholate) before elution (20 mM Tris-HCl pH 7.5, 5 mM EDTA, 50 mM NaCl, and 1% SDS), reverse cross-linking, and subsequent DNA extraction. ChIP-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions, and then sequenced on a HiSeq X Ten platform (Illumina). For data analysis, the sequences with adaptor and low quality were trimmed for all 150-bp pair-end reads. The clean reads were mapped against the human reference genome (GRCh37/hg19) using BWA (Li and Durbin, 2009). All the samples were separately processed, and the unique mapped reads were kept. The peaks were called by MACS2 (v2.1.1) (Zhang et al., 2008) using IgG as control. The results were analyzed and visualized in IGV (v2.8.6) (Thorvaldsdottir et al., 2013). For 4C-seq, 4C assays were conducted as previously represented (Splinter et al., 2012; van de Werken et al., 2012b) with modifications. Briefly, SC cells were counted, and ~1 × 107 cells were used for each 4C experiment. The cells were cross-linked with 1.5% formaldehyde, quenched with 0.125 M glycine, lysed with cold lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, and 1× Protease Inhibitors), digested with DpnII (NEB, R0543M) for 4 h at 37°C while shaking at 900 rpm for more than 3 times until the digestion efficiency reached over 90%, and then ligated with T4 DNA ligase (NEB, M0202M) in a 7 ml reaction system after enzyme inactivation. After reversing the cross-links by adding Protein K (ThermoFisher, AM2548) for overnight at 65°C and RNase A for 45 min at 37°C, the ligation products were purified by Phenol/Chloroform/Isoamyl Alcohol (25:24:1) (ThermoFisher, 15593-049). The purified DNA samples were digested with NlaIII (NEB, R0125L) for the rs4728142-containing region (GRCh37/hg19 chr7: 128,573,714–128,574,084) or CviQI (NEB, R0639L) for the enhancer (GRCh37/hg19 chr7: 128,573,036–128,573,717) adjacent to the downstream rs4728142-containing region, and then ligated with T4 DNA ligase for overnight in a 14 ml reaction system. The ligation samples were purified by Phenol/Chloroform/Isoamyl Alcohol (25:24:1) and further purified utilizing the QIAquick PCR Purification Kit. The purified products were amplified by VAHTS HiFi Amplification Mix (Vazyme, N616) with 8 × 200 ng DNA. 4C-seq libraries were generated using the VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the kit’s instructions and then sequenced on a HiSeq X Ten platform. For data analysis, the quality control step was processed for the 4C-seq library using FastQC. The sequences with adaptor and low quality were discarded for further analysis. A Bioconductor package Basic4Cseq (Walter et al., 2014) was used to filter, analysis, and visualize the 4C-seq data. For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Human peripheral blood monocyte-derived SC cells


title: genomic DNA from buccal swab 540 [201557550033_R08C01]

description: human buccal swab

value: Physical Risk


title: genomic DNA from buccal swab 539 [201557550033_R07C01]

description: human buccal swab


title: genomic DNA from buccal swab 537 [201557530002_R03C01]

description: human buccal swab


title: T cell rep2

status: Public on Jan 06 2021

data_processing:
data was processed using the ENCODE ATAC-seq Pipeline version 1.4.2
Parameters for pipeline were:  atac.multimapping=0, atac.smooth_win=150, atac.enable_idr=true, atac.idr_thresh=0.1
Master peaklist was generated by chromVAR v1.02 and the filterPeaks function using default parameters
Peaks were annotated using annotatePeaks.pl function in HOMER v4.10.2
Genome_build: mm10
Supplementary_files_format_and_content: Annotated Master peak-list output from chromVAR and HOMER

source_name: thymus

growth_protocol: Adult (8-12 weeks old) Wild-type C57/Bl6 mice were sacraficed and cells were harvested from  bone marrow and/or thymus.

extract_protocol:
Cells were collected after sorting into microcentrifuge tubes containing staining media (1xDPBS,1mM EDTA with 5% serum) and centrifuged at 500xg for 5 minutes at 4˚C . Cell pellet was washed with ice-cold 1xDPBS and centrifuged as above. Cells were lysed in (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and centrifuged at 500xg for 10 minutes. Samples were suspended 25µL 2xTD Buffer, 2.5µL transposase (Illumina), and 22.5µL nuclease free water and incubated at 37˚C for 30 minutes at 600rpm. Samples were purified using the MinElute Reaction Clean up kit (Qiagen).
Library fragments were amplified using NEBnext PCR mastermix and custom Nextera primers, and size selected using Ampure XP Beads.

treatment_protocol: Bone marrow or thymic cells were stained with flourescent antibodies and sorted by FACS according to established markers.

value: T Cell


title: SC cells-rs4728142-4C-seq


title: B cell rep2

source_name: bone marrow

value: B Cell


title: genomic DNA from buccal swab 538 [201557550033_R01C01]

description: human buccal swab


title: Lens Epithelium from Male Aged Mice, 24 Hours post surgery, rep 1

description:
A_24_hr_1M_S69
AllEpi_AE24vYE24_ExactTestQVL_Differential_Expression.xlsx
AllEpi_AE24vAE0_ExactTestQVL_Differential_Expression.xlsx


title: B cell rep1


title: GM rep2

value: Granulocyte/Macrophage


title: EP rep1

value: Erythrocyte Progenitor


title: GM rep1


title: MkP rep1


title: T cell rep1


title: 057ACEAC_sequence

status: Public on Dec 30 2020

city: San Francisco

first: Srilaxmi

last: Nerella

state: CA

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

description:
Messenger RNA from single cell preparations
Independent sample
057ACEAC_sequence

data_processing:
UMI-based gene expression quantification, using Cell Ranger (Version 3.0, 10X Genomics, Pleasanton, CA)
Alignment to the hg38 human genome
Subsequent analyses using Seurat v3.0 in R
Genome_build: hg38 human genome
Supplementary_files_format_and_content: Cell Ranger output

source_name: Bronchial cells from human airway epithelial brushings

growth_protocol: Epithelial brushings were obtained at bronchoscopy

extract_protocol:
10X Chromium Controller
10X Chromium Next GEM Single Cell 3’GEM, Library & Gel Bead Kit (V3)

treatment_protocol: Epithelial brushings preparations were diaggregated using ACCUMAX. Cells were resuspended and stored resuspend in 50K aliquots using Fluidigm 10X freezing solution (minimum volume of 250 uL) at -80 in a cooling rack then transfer to liquid N2

value: Bronchial cells

tag: diagnosis

value: asthma

tag: treatment

value: Post-Allergen Challenge (cat)


title: HSC rep1

value: Hematopoietic Stem Cell


title: 057ACEDIL_sequence

description:
Messenger RNA from single cell preparations
Independent sample
057ACEDIL_sequence

value: Post-Diluent Challenge


title: 049ACEAC_sequence

description:
Messenger RNA from single cell preparations
Independent sample
049ACEAC_sequence

value: Post-Allergen Challenge (house dust mite)


title: 044ACEAC_sequence

description:
Messenger RNA from single cell preparations
Independent sample
044ACEAC_sequence


title: EoE-12.tRNA.EoE

status: Public on Aug 22 2020

description:
EREFS 3
lib29316_CCFMDANXX

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the TopHat aligner (v1.4.1)28 with the GRCh38 reference genome and gene annotations from ensembl release 77.
Gene counts were generated using HTSeq-count (v0.4.1)29. Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2)30, and HTSeq-count (v0.4.1).
Genome_build: GRCh38 reference genome and gene annotations from ensembl release 77
Supplementary_files_format_and_content: Processed data (counts) are in .csv format. Each row is a gene, each column is a sample.

source_name: esophageal tissue

growth_protocol: Biopsies were collected in RNAlater (Thermo Fisher Scientific) and paired blood samples were collected in Tempus Blood RNA Tubes (Thermo Fisher) and stored at -80◦C until use.

extract_protocol:
Total RNA was isolated from adult esophageal biopsies (1-2 per subject) by homogenizing tissue in QIAzol lysis reagent (Qiagen) followed by column purification using the miRNeasy kit with on column DNA digestion (Qiagen). Whole blood RNA was extracted using MagMax for Stabilized Blood Tubes RNA Isolation Kit, followed by globin reduction using GlobinClear Human (Thermo Fisher).
Sequencing libraries were constructed from total RNA using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and NexteraXT DNA sample preparation kit (Illumina) to generate Illumina- compatible barcoded libraries.
Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.

tag: study group

value: EoE

tag: eosinophils per high-powered field


title: Non differentiated cells

status: Public on Dec 29 2020

city: Mexico City

first: Federico

last: Castro-Muñozledo

address: Av Instituto Politecnico Nacional 2508, San Pedro Zacatenco

department: Cell Biology

country: Mexico

institute: CINVESTAV

data_processing:
Quality evaluation of raw reads, adapter removal and pairing of reads were carried out using the Geneious workflow software (Geneious version 9.1.8).
Paired reads were mapped to the reference genome OryCun2.0; GCF_000003625.3, using the Geneious for RNAseq mapper.
Differential expression (DE) analysis was carried out using the Geneious tools, calculating expression measures TPM, RPKM and FPKM normalized by the Median of Gene Expression Ratios method.
Genome_build: oc2 GCF_000003625.3
Supplementary_files_format_and_content: tab-delimited text file including expression values for each sample

organism: Oryctolagus cuniculus

source_name: Corneal epithelium

growth_protocol: Cells were seeded at 2.7 x 103 cells/cm 2 together with mitomycin C-treated 3T3 cells plated at 2.2 x 104 cells/cm2, as previously described (Castro-Muñozledo, 1994, J Cell Sci 107, 2343-2351). Cells were cultured using the mixture DMEM-F12-Ham (3:1) supplemented with 5% fetal calf serum, 5 µg/ml insulin, 5 µg/ml transferrin,  0.4 µg/ml hydrocortisone, 2×10−9 M triiodothyronine, 1×10−10 M cholera toxin, 24.3 mg/l adenine and 10 ng/ml epidermal growth factor (EGF). Medium was changed every other day. Cultures were maintained at 36° C in a 10% CO2 and 90% air humidified atmosphere.

extract_protocol:
Before RNA isolation, the 3T3-feeder cells were removed by a 5-min incubation with 0.02% (w/v) EDTA  in PBS. Samples were washed twice with PBS; afterwards, total RNA was isolated at 4th, 6th and 10th days in culture with Trizol reagent according to the instructions of the manufacturer, then resuspended in DNase/RNase free water.
cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer’s instructions.

tag: cell line

tag: tissue

value: Corneal epithelium

tag: time point

value: 4 days


title: EoE-08.tRNA.EoE

description:
EREFS 3
lib29315_CCFMDANXX


title: Terminal differentiated cells

value: 10 days


title: EoE-11.tRNA.EoE

description:
EREFS 6
lib29314_CCFMDANXX


title: EoE-13.tRNA.not EoE

description:
EREFS 0
lib29311_CCFMDANXX

value: not EoE


title: EoE-07.tRNA.not EoE

description:
EREFS 3
lib29312_CCFMDANXX


title: EoE-10.tRNA.not EoE

description:
EREFS 0
lib29313_CCFMDANXX


title: EoE-06.tRNA.not EoE

description:
EREFS 0
lib29310_CCFMDANXX


title: EoE-01.tRNA.not EoE.lymphocytic esophagitis

description:
EREFS 0
lib29308_CCFMDANXX


title: EP rep2

tag: cell type


title: EoE-05.tRNA.EoE

description:
EREFS 8
lib29309_CCFMDANXX

tag: age


title: EoE-02.tRNA.EoE

description:
EREFS 3
lib29307_CCFMDANXX


title: EoE-11.whole blood.EoE

description:
EREFS 6
lib29304_CCFMDANXX

source_name: whole blood


title: HSC rep2

tag: strain


title: MkP rep2

value: Megakaryocyte Progenitor


title: EoE-08.whole blood.EoE

description:
EREFS 3
lib29305_CCFMDANXX


title: EoE-12.whole blood.EoE

description:
EREFS 3
lib29306_CCFMDANXX


title: EoE-07.whole blood.not EoE

description:
EREFS 0
lib29302_CCFMDANXX


title: EoE-05.whole blood.EoE

description:
EREFS 8
lib29299_CCFMDANXX


title: EoE-13.whole blood.not EoE

description:
EREFS 0
lib29301_CCFMDANXX


title: EoE-06.whole blood.not EoE

description:
EREFS 0
lib29300_CCFMDANXX


title: EoE-01.whole blood.not EoE.lymphocytic esophagitis

description:
EREFS 0
lib29298_CCFMDANXX


title: EoE-02.whole blood.EoE

description:
EREFS 3
lib29297_CCFMDANXX


title: 049ACEDIL_sequence

description:
Messenger RNA from single cell preparations
Independent sample
049ACEDIL_sequence


title: Committed cells

value: 6 days


title: RNA-seq rep2

status: Public on Jul 22 2020

city: Cincinnati

first: Maria

middle: M.

last: Mikedis

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Base calls were performed by the instrument control software and further processed using the Offline Base Caller (Illumina) v.1.9.4. Quality control/assessment was performed using fastqc, fastqscreen and custom scripts.
Reads were quality-trimmed with cutadapt v.1.8 using the following options: -q 20 -m 24
Libraries were mapped to the mouse genome (mm10) via STAR v.2.5.4b (Dobin et al., 2013) (options: --outFilterMultimapNmax 1 --alignEndsType Extend5pOfRead1 --outFilterMismatchNmax 2 --outSAMattributes None). All other parameters were set to default. Full mapped reads were then used as background RNA-seq for calling DAZL iCLIP peaks via ASPeak v.2.0.0
To quantify transcript abundance, expression levels of all transcripts in the UCSC RefSeq (refGene) transcript annotations and Retrogenes V6 annotations from the GRC38 (mm10) assembly were estimated using kallisto v.0.44.0 (Bray et al., 2016) with sequence-bias correction using a 31 k-mer index. These values are in *RNAseq_abundance.tsv files. See annotation file mm10_GRCm38_refGene_retrogenes_annotation.file.txt
For the comparison of biological replicates and iCLIP analysis, rRNA transcripts were removed, and TPM values were renormalized to transcript-per-million units. TPM values were summed to the gene level, with protein-coding transcripts and non-coding transcripts from the same gene summed separately. These values are in *RNAseq_no.rRNA_abundance.tsv files. See annotation file mm10_GRCm38_refGene_retrogenes_no.rRNA_annotation.file.txt
For comparison to other publically available datasets, quantified transcripts were filtered for refGene transcripts (excluding rRNA), and TPM values were renormalized to transcript-per-million units. These values are in *RNAseq_refGene.no.rRNA_abundance.tsv files. See annotation file mm10_GRCm38_refGene_no.rRNA_annotation.file.txt
For translational profiling via RIboTag IP-seq, quantified transcripts were filtered for protein-coding mRNAs only, and TPM values were renormalized to transcript-per-million units. These values are in *RNAseq_coding.mRNA.only_abundance.tsv files. See annotation file mm10_GRCm38_refGene_coding.mRNA.only_annotation.file.txt
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with the following fields: target_id length, eff_length, est_counts, tpm

source_name: undifferentiated spermatogonia-enriched postnatal testes

extract_protocol:
Undifferentiated spermatogonia from a single chemically synchronized postnatal animal were used as one biological replicate; two biological replicates were carried out in total. RNA was extracted using Trizol LS (Thermo Fisher Scientific) and chloroform following the manufacturer’s protocol, precipitated via isopropanol with GlycoBlue (Thermo Fisher Scientific), and resuspended in RNase-free water.
TruSeq Stranded mRNA kit (Illumina) with RiboZero depletion

treatment_protocol: Spermatogenesis was chemically synchronized and undifferentiated spermatogonia were sorted as previously described (Romer et al., 2018 Developmental Biology). Specifically, on postnatal days (PND) 2-8, ROSA26tdTomato/+; Ddx4Cre/+ male mice were injected daily subcutaneously with WIN 18,446 (Santa Cruz Biotechnology) at 0.1mg/gram body weight. On PND9, mice were euthanized to obtain testes enriched for undifferentiated spermatogonia.  Testes were \biopsied for histological analysis to verify enrichment of undifferentiated spermatogonia. For the remaining testis pair, the tunica albuginea was removed, and the tissue was dissociated into a single-cell suspension using collagenase and trypsin as previously described (Romer et al., 2018) with one modification: TURBO DNAse was used in place of DNAse I. DAPI was added to cells prior to cell sorting on a FACSAria II (BD Biosciences). Single cells were gated based on forward and side light scatter, and high DAPI-positive (dead) cells were excluded. The undifferentiated spermatogonia were isolated based on tdTomato fluorescence, whose expression was activated by the germline-specific Ddx4Cre, and sorted in 1% BSA in PBS. Cells were transferred into and stored at  -80˚C in Trizol LS (Thermo Fisher Scientific).

tag: genotype

value: ROSA26tdTomato/+; Ddx4Cre/+

value: spermatogonia