title: WT KDS1 + MMC rep2 - ChIP

city: Ann Arbor

first: Yulduz

last: Rakibova

state: MI

address: 1150 W Medical center drive

department: Biological Chemistry

institute: University of Michigan

data_processing:
For IPOD, INPUT and ChIP-seq: ipod singularity container version 2.7.2 was used (available at https://github.com/freddolino-lab/ipod). Peak calling was done with version 2.8.1
Assembly: We obtained an initial genome reference sequence for KDS1 by sequencing high molecular weight genomic DNA purified from the strain. Raw reads are available at SRA########. Initial assembly was performed on the Nanopore reads using NECAT (version 0.0.1 20200803), resulting in two contigs which clearly correspond to the two V. cholerae chromosomes. The assembly was then polished using pilon (version 1.24) using default arguments, with all available reads from INPUT samples (aligned using bowtie2) as the short read inputs. Manual finishing was performed using a set of iterative rounds of breseq (version 0.37.0) runs to identify remaining discrepancies between the Illumina short read data and the in-progress assembly and resolving them by applying differences with gdtools. We then manually assigned the starting position of each chromosome to match those of commonly used El Tor reference genomes.  Annotation of the newly obtained assembly was performed using prokka (version 1.14.5) with arguments --genus Vibrio --species cholerae --accver 2, using a draft genome obtained from the ***** as a reference for potential proteins. We then assigned VC numbers to all identifiable genes matching the reference El Tor strain (EMBL reference sequences AE003852.1 and AE003853.1 for chromosomes 1 and 2, respectively). Annotated genes from the El Tor reference were aligned to those of our prokka-annotated KDS1 assembly, using nucmer (v. 3.1) with default settings. We further required that for each potential match, the starting and ending positions of the reference El Tor version and the KDS1 version in the identified features differed by no more than 20 nucleotides.
Supplementary files format and content: Files with suffix _IPOD_rzchipsub_rep*.bedgraph are four-column bedgraph files with the first column representing the reference genome, second – start coordinate in 5nt increments and third – end coordinate in 5nt increments, and the fourth column represents the occupancy robust z-score of quantified total protein occupancy with RNA ChIP-seq subtracted. The robust z-scores are given for each 5 nucleotides on the genome. The rep* represents the replicate number for the sample
Supplementary files format and content: Files with suffix _IPOD_vs_inp_rzlograt_rep*.bedgraph are four column bedgraph files with the first column representing the reference genome, second -- start coordinate in 5nt increments and third – end coordinate in 5nt increments, and the fourth column represents the robust z-score of quantified total protein occupancy. The robust z-scores are given for each 5 nucleotides on the genome. The rep* represents the replicate number for the sample
Supplementary files format and content: Files with suffix _CHIP_vs_inp_rzlograt_rep*.bedgraph are four column bedgraph files with the first column representing the reference genome, second – start coordinate in 5nt increments and third – end coordinate in 5nt increments, and the fourth column represents the robust z-score of quantified RNA polymerase ChIP-seq. The robust z-scores are given for each 5 nucleotides on the genome. The rep* represents the replicate number for the sample
Supplementary files format and content: EPODs: file KDS1_IPOD_rzchipsub_mean_epods_strict.bedgraph represents called strict EPODs by the IPOD pipeline and represents the extended protein occupancy regions based on protein occupancy with RNA polymerase ChIP-seq subtracted in each of the conditions (IPOD-HR). The file is a bedgraph file where the first column is the reference genome chromosome, second – start and third – end coordinates on the genome in 5 nucleotide intervals, and fourth – 1 or 0 for whether the position is an EPOD (1) or not (0)
Supplementary files format and content: inverted EPODs (nEPODs): file KDS1_IPOD_vs_inp_rzlograt_mean_inverted_epods_strict.bedgraph represents called strict inverted EPODs by the IPOD pipeline and represents the extended negative protein occupancy regions based on total protein occupancy negative scores in each of the conditions (IPOD). The file is a bedgraph files where the first column is the reference genome chromosome, second – start and third -- end coordinates on the genome in 5 nucleotide intervals, and fourth – 1 or 0 for whether the position is an inverted EPOD (i.e. nEPOD; 1) or not (0)
Supplementary files format and content: KDS1_IPOD_vs_inp_rzlograt_inverted_strict_merged_epods.narrowpeak and KDS1_IPOD_rzchipsub_strict_merged_epods.narrowpeak are narrowpeak files where the columns represent: col 1 – reference genome chromosome, col 2 – start and col 3 – end coordinates of merged EPODs from each replicate of IPOD-HR samples. The files are generated from IPOD pipeline, see https://github.com/freddolino-lab/ipod for details.
Supplementary files format and content: Peak calls: files with suffix _idr_passed.narrowpeak are called peak files generated from our IPOD pipeline, see  https://github.com/freddolino-lab/ipod for details.
Library strategy: IPOD-HR which include ChIP-seq and IPOD

organism: Vibrio cholerae

growth_protocol: All standard overnight bacterial cultures were grown from a single colony in 2 mL volume with aeration at 37C in standard LB Miller liquid growth medium, supplemented with streptomycin (100 µg/mL). For cultures requiring mitomycin C treatment, an overnight culture grown in standard conditions was diluted to an OD600 of 0.003 into 140 mL of pre-warmed LB Miller liquid medium supplemented with mitomycin C to a final concentration of 20 ng/mL. Cultures were grown to a final OD600 of 0.3.

extract_protocol:
IPOD sample preparation. IPOD samples were collected as previously described (Freddolino PL et al, PLoS Biology, 2022) with minor modifications. Overnight cultures were diluted to a starting OD600 of approximately 0.003 in a final volume of 140 mL of LB medium in a 1 L flask. The diluted cultures were grown at 37C with shaking at 250 RPM until a final OD600 of 0.3. 28.9 mL of culture was collected at each time point and mixed with 300 μL 1 M sodium phosphate buffer (pH 7.4) and 810 μL formaldehyde (37%, fresh) in a 50 mL conical tube, then allowed to crosslink for 5 minutes shaking at room temperature (notably, unlike in Freddolino PL et al, no rifampicin was added prior to crosslinking). After 5 minutes, the crosslinking reactions were quenched with 6 mL of 2M glycine and returned to the room temperature shaker. After 10 minutes of shaking, tubes were placed in ice for 10 minutes and then pelleted at 7,000x g at 4C for 4 minutes. Pellets were washed twice with 10 mL of ice-cold phosphate-buffered saline and the final cell pellets were snap-frozen in a dry ice-ethanol slurry and stored at -80C. Cell lysis, digestion, and lysate clarification. The original IPOD-HR protocol is from ref. (Freddolino PL et al, PLoS Biology, 2022); below we summarize the procedures applied here. Frozen cell pellets were resuspended in 600 μL of 1X IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) with 1x protease inhibitors tablet (Roche Complete Mini, EDTA free, Roche Diagnostics GmbH, Mannheim, Germany) and 1.5 μL lysozyme (ThermoScientific, REF90082, 50 mg/mL) incubated for 15 minutes at 30C with gentle shaking and then placed on ice. Resuspended cells were sonicated with a Branson sonicator at 25% power with three bursts of 10s ON and 10s OFF while in an ice water bath. Sonicated cells were then digested with 6μL RNaseA (SIG 10109169001, Sigma-Aldrich/Roche, 10mg/mL), 5.4 μL  of 100mM MnCl2, 4.5 μL of 100mM CaCl2, 9 μL of DNase I, RNAse-free (ThermoScientific, #89836, 1U/μL) and incubated on ice for 30 minutes, after which reactions were quenched with 50 μL 500mM EDTA (pH 8.0); we aimed to obtain fragment sizes of about 150 bp. 400 μL of 1x IPOD lysis buffer without protease inhibitors and lysozyme was added to the digested mixture and vortexed. The mixture was clarified by centrifugation for 10 minutes at 15,700 x g at 4C and transferred to new tubes. The clarified lysate was partitioned into three different tubes: 50 μL for INPUT (for baseline reference), 400 μL for IPOD (for total protein occupancy), and the rest for CHIP (for RNA polymerase occupancy). 450 μL of ChIP elution buffer (50mM Tris (pH 8.0), 10mM EDTA, 1% SDS) was added to the INPUT sample and kept on ice until reverse cross-linking step (mentioned in the next step). Cell lysis, digestion, and lysate clarification. The original IPOD-HR protocol is from ref. (Freddolino PL et al, PLoS Biology, 2022); below we summarize the procedures applied here. Frozen cell pellets were resuspended in 600 μL of 1X IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) with 1x protease inhibitors tablet (Roche Complete Mini, EDTA free, Roche Diagnostics GmbH, Mannheim, Germany) and 1.5 μL lysozyme (ThermoScientific, REF90082, 50 mg/mL) incubated for 15 minutes at 30C with gentle shaking and then placed on ice. Resuspended cells were sonicated with a Branson sonicator at 25% power with three bursts of 10s ON and 10s OFF while in an ice water bath. Sonicated cells were then digested with 6μL RNaseA (SIG 10109169001, Sigma-Aldrich/Roche, 10mg/mL), 5.4 μL  of 100mM MnCl2, 4.5 μL of 100mM CaCl2, 9 μL of DNase I, RNAse-free (ThermoScientific, #89836, 1U/μL) and incubated on ice for 30 minutes, after which reactions were quenched with 50 μL 500mM EDTA (pH 8.0); we aimed to obtain fragment sizes of about 150 bp. 400 μL of 1x IPOD lysis buffer without protease inhibitors and lysozyme was added to the digested mixture and vortexed. The mixture was clarified by centrifugation for 10 minutes at 15,700 x g at 4C and transferred to new tubes. The clarified lysate was partitioned into three different tubes: 50 μL for INPUT (for baseline reference), 400 μL for IPOD (for total protein occupancy), and the rest for CHIP (for RNA polymerase occupancy). 450 μL of ChIP elution buffer (50mM Tris (pH 8.0), 10mM EDTA, 1% SDS) was added to the INPUT sample and kept on ice until reverse cross-linking step (mentioned in the next step). Interphase extraction and nucleic acid purification. 400 μL of 100 mM Tris Base and 800 μL of 25:24:1 phenol:chloroform:isoamyl alcohol (Sigma Aldrich, #77617) was added to the 400 μL of clarified lysate kept for the IPOD-HR sample, vortexed for 10s, and then incubated for 10 minutes at room temperature. To obtain a separation of the organic and aqueous layers and formation of the white interphase disc, which is enriched in protein-DNA complexes, the mixture was spun for 2 minutes at 21,130 x g at room temperature. The aqueous and organic layers around the interphase were removed while minimizing disturbance of the interphase disc. The extracted disc was washed once in 350 μL TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 μL 100 mM Tris base, and 700 μL 24:1 chloroform:isoamyl alcohol. The layers were again separated by spinning for 2 minutes at 21,130 x g at room temperature. After removal of liquid around the interphase disc, a  final wash of 700 μL TE and 700 μL 24:1 chloroform:isoamyl alcohol was applied. After vortexing and spinning the final wash as before, as much of the liquid around the white disc as possible was removed and discarded. The interphase disc was resuspended in 500 μL of ChIP elution buffer and vortexed. The resuspended interphase of IPOD sample and INPUT sample (kept on ice from above step) were incubated at 65C overnight to reverse-crosslink (6-16 hours). RNA Polymerase Chromatin Immunoprecipitation. The rest of the clarified lysate (about 500 μL) was mixed with 1 volume of 2x immunoprecipitation (IP) buffer (200mM Tris (pH 8.0), 600mM NaCl, 4% Triton X-100) and incubated with 10μg of anti-E. coli RNA polymerase antibody (NeoClone WP023, NeoClone, Madison, WI, Lot: 2019G15-002) overnight with rocking at 4C. After overnight incubation, 50 μL of protein G beads (New England Biolabs (NEB), S1430S) per sample was equilibrated in 1x IP buffer. 50 μL of equilibrated protein G beads was added to each antibody-lysate mixture and then incubated with rocking 2 hours at 4C. After incubation, the beads were washed once in 1mL of the following buffers: IP wash buffer A, IP wash buffer B, IP wash buffer C, 1x IP buffer, and 1x TE.  1x wash buffer A (100mM Tris, pH 8.0; 250mM LiCl; 2% Triton X-100; 1mM EDTA) 1x wash buffer B (10mM Tris, pH 8.0; 500mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1mM EDTA) 1x wash buffer C (10mM Tris, pH 8.0; 500mM NaCl; 1% Triton X-100; 1mM EDTA) After the wash steps, beads with the immunoprecipitated material were resuspended in 500 μL of ChIP elution buffer by rocking for 5 minutes; the samples were then incubated for 30 minutes at 65C with vortexing every 5 minutes. The beads were then separated and discarded to retain only the eluted immunoprecipitated sample. The samples were then left to reverse-crosslink overnight (6-16 hours) at 65C. DNA extraction post reverse cross-linking. The DNA from INPUT, IPOD, and ChIP samples were isolated and purified following identical steps. After overnight incubation to reverse the formaldehyde crosslinks, each sample was incubated with 10 μL of RNAse A (Roche Diagnostics GmbH, #SIG10109169001, 10mg/mL) for 2 hours at 37C. Then we followed by adding 10 μL Proteinase K (ThermoScientific, #EO0491, 20mg/mL) and incubating for 2 hours at 50 oC. The DNA of each sample was isolated by phenol-chloroform extraction using one volume of 25:24:1 phenol:chloroform:isoamyl alcohol, then re-extracted with one volume of 24:1 chloroform:isoamyl alcohol. At the last stage the samples went into DNA LoBind tubes. The isolated DNA was then precipitated by adding 1/25th volume of 5M NaCl as a precipitating salt, 1/300th volume of GlycoBlue (Invitrogen, #AM9515, 15mg/mL) as a co-precipitant, and two volumes of ice cold 1:1 isopropanol:ethanol. The DNA was precipitated at 4C for one hour and at -20C for more than 1 hour or overnight.  Chilled samples were then centrifuged for 15 minutes at 16,100 x g at 4C to pellet the DNA. All the liquid was then removed without disturbing the DNA pellet. Pellets were then washed in freshly diluted 95% ethanol, vortexed and then centrifuged for 5 minutes at 16,100 x g at 4C. Finally, the liquid was removed, and the remaining ethanol was left to evaporate for 30 minutes or less. The following volumes of TEe (10 mM Tris, pH 8.0; 0.1 mM EDTA) were added to resuspend the DNA from the three sample types: 200 μL for INPUT pellets, 50 μL for IPOD, and 30 μL for ChIP. All samples were quantified with QuantiFluor dsDNA System (Promega, #2670) using a BioTek Synergy plate reader. Input samples were assessed for fragment sizes on 2% agarose gel electrophoresis.
Illumina library preparation for IPOD-HR. The purified and quantified DNA from INPUT, IPOD, and RNA Polymerase ChIP samples were then prepared for Illumina sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#7645S/L) with NEBNext® Multiplex Oligos for Illumina® Unique Dual Index UMI Adaptors DNA Set 1 (#E7395S) or NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (#E7600S) and Dual Index Primers Set 2 (#E7780S). Omega Biotek Mag-Bind DNA purification or Axygen purification beads were used for all SPRI bead cleanup steps. The bead purification at the post-adaptor ligation stage was modified as follows: 1.8x volume of DNA purification beads and 0.7x isopropanol were added instead of the normal 0.9x volume of beads.  Each sample prepared for sequencing was quantified and assessed for fragment size and for the presence of any adaptor present on 2% agarose gel electrophoresis. The samples were pooled into libraries, which were sequenced on a NextSeq 550 instrument at the Michigan Advanced Genomics Core.

value: wild type

tag: media

value: LB + Mitomycin C

tag: chip antibody

value: anti-RNA polymerase antibody (NeoClone WP023)

tag: time of_harvest

value: logarithmic phase


title: AB7095

status: Public on Feb 09 2024

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: MARSseq

library_source: transcriptomic single cell

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
LSK cells were single-cell sorted from mice 4 weeks after transplantation by flow cytometry.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: control (CD45.1) and Regnase-1–/–Regenase-3–/– (CD45.2) fetal liver cells were 1:1 mixed and transfered into lethally-irradiated mice (CD45.1/CD45.2).

tag: cell type

value: LSK

tag: tissue

value: bone marrow

tag: strain


title: AB7094

description: MARSseq


title: SIC_121_Colon_382_CD45pos_5p_GEX

city: Charlestown

first: Kamil

last: Slowikowski

state: Massachusetts

address: Mailstop CNY 149-8, 149 13th Street

country: USA

institute: Massachusetts General Brigham

data_processing:
We used Cell Ranger v3.1.0 for generating gene count matrices from sequencing reads (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). We used R scripts to analyze the count matrices.
Assembly: GRCh38-3.0.0
Supplementary files format and content: H5 files, anndata h5ad files, HTML files, CSV files

organism: Homo sapiens

source_name: Colon mucosal biopsy

extract_protocol:
Please see the methods in the associated publication.
Please see the methods in the associated publication.

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)

tag: chemistry


title: Scar, WTTR, 3

city: Tainan City

first: Yi-Kai

last: Hong

state: Please select an option below

address: No.1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

library_source: transcriptomic

data_processing:
The bases with low quality were removed using fastp software (version 0.20.0).
Alignment was performed by hisat2 software (version 2.1.0) with a reference of GRCm38.
Reads were counted by featureCounts software (version 2.0.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw reads for each sample

source_name: scar

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

tag: genotype

tag: treatment

value: Traction

value: hypertrophic scar-like animal model using traction force

value: scar


title: Scar, lacZSH, 2

value: Sham


title: AB7093

description: MARSseq

tag: cell type


title: SIC_126_Colon_398_CD45pos_5p_GEX

tag: tissue


title: WT KDS1 + MMC rep1 - ChIP

library_source: genomic

molecule: genomic DNA

tag: strain

value: wild type

tag: media

tag: chip antibody

tag: time of_harvest


title: SIC_109_Colon_368_CD45pos_5p_GEX

tag: patient id

tag: simplified patient_id

tag: disease state

value: Control - On ICI Therapy

tag: steroids at_the_time_of_biopsy


title: Scar, lacZSH, 1


title: WT KDS1 + MMC rep2 - INPUT

value: LB + Mitomycin C


title: Scar, WTSH, 2


title: SIC_100_Colon_332_CD45sort_5p_GEX

tag: initial vs_follow_up_sample

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Frozen

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: AB7092

description: MARSseq

value: LSK

value: bone marrow


title: WT KDS1 + MMC rep2 - IPOD

value: logarithmic phase


title: WT KDS1 + MMC rep1 - INPUT


title: MC_9_Colon_661_CD45sort_5p_GEX

value: Colon mucosal biopsy

value: Control - Healthy

value: Initial

tag: rbc depletion_methods

tag: dead cell_depletion_method

tag: cd45 positive_selection

tag: chemistry


title: WT KDS1 + MMC rep1 - IPOD

tag: genotype


title: Δihfa KDS1 rep1 - ChIP

tag: strain

value: {delta}ihfA

value: LB

value: anti-RNA polymerase antibody (NeoClone WP023)


title: MC_2_Colon_576_CD45sort_5p_GEX_A

tag: tissue

value: Fresh


title: SVZ_2

city: Madison

first: Darcie

middle: L.

last: Moore

state: WI

address: 1111 Highland Ave

department: Neuroscience

institute: University of Wisconsin-Madison

description: SORTseq

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for the identification of the Illumina library barcode, cell barcode, and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA (0.7.15) with default parameters. The data was demultiplexed to single-cells as described in Grün et al. 2014. Mapping and generation of count tables were automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo). The information from Read1 was transferred to the header in Read2 fastq files.
The data from all samples were loaded in R (version 4.2.0) and processed using the Seurat package (version 4.1.1 – Hao et al. Cell 2021). More specifically, cells with at least 1000 UMI’s per cell and less than 10% mitochondrial gene content were retained for analysis. The dataset was normalized for sequencing depth per cell, log-transformed using a scaling factor of 10,000.
Assembly: mm10
Supplementary files format and content: Comma-separated file
Supplementary files format and content: Tab-separated file

molecule: polyA RNA

source_name: Subventricular zone

extract_protocol:
8 male Envigo C57BL/6J  mice per experiment were used to sort cells from the SVZ. Using a modified previously published protocol for dissection, SVZ tissue was dissected into cold HBSS without Ca2+ and Mg2+, followed by mincing of the tissue with a razor blade. Tissue was resuspended in 0.05% Trypsin-EDTA, and put in a 37 degrees C water bath for 6 minutes. Trypsin was quenched using a double volume of pre-warmed trypsin inhibitor including DNAse, and centrifuged for 300xg for 5 minutes. The pellet was resuspended in a cold, sterile-filtered, 0.5% BSA/PBS solution (sort buffer) and dissociated by pipetting 20 times up/down. A 45µM mesh filter was pre-wet with the same solution, and the run-through discarded. The brain sample was run through the filter, followed by a 1ml rinse. The cell solution was spun for 300xg for 5 minutes for 4 degrees C. All spins and treatments from this point forward were performed at 4 degrees C.  For 2 of the 3 experiments, myelin was removed using a Miltenyi Magnetic sorting protocol. In short, the appropriate volume of cold sort buffer was added based on weight, as well as myelin removal beads, followed by incubation for 15 minutes in the refrigerator. After washing, lysate was centrifuged at 300xg for 10 minutes. The pellet was resuspended in sort buffer, and then was filtered through the magnetic column. The effluent was spun down, and then resuspended in sort buffer and an anti-GLAST-Biotin antibody (Miltenyi), incubating for 10 minutes in the refrigerator. Following wash and centrifugation, cells were further labeled with anti-biotin microbeads (Miltenyi) for 15 minutes in the refrigerator. To prepare cells for loading onto the magnetic column, they were washed, centrifuged, and resuspended in sort buffer. Cells that were GLAST+ were on beads that remained in the column on the magnetic plate. The column was washed, and beads and cells eluted into a collection tube using a plunger once removed from the magnetic plate, centrifuged, and resuspended in an ice-cold staining buffer containing L-15, 1M HEPES 7.4 pH, 100x Pen-strep, and 100mM EDTA. CD24-APC-eFluor780 (M16947-0242-82; 1:200) and O4-Cy7 (Miltenyi – 130-115-810; 1:200) were added for a total of 45 minutes, with CD133-APC (Clone 13A6; 1:50) added in the final 25 minutes of incubation on ice. Cells were then washed and centrifuged, and resuspended in FACS buffer with 4µg/ml DNAse, and transported to the FACS machine on ice. There, using previously established compensated settings, GLAST+ (per bead sorting) CD133+ (low to middle intensity) CD24-, O4- (together labeled in the same “dump” channel) were sorted into a 384 well plate, with autofluorescence intensity measured for each cell. To establish the compensated settings, cells collected from the brain were singly labeled for each antibody, and then as a group. Viable single cells were FACS sorted into 384-well plates, snap frozen, and sent to Single Cell Discoveries for processing and analysis.  This experiment was performed 3 separate times, collecting cells from each experiment to be analyzed together.
Libraries for each plate were prepared according to an adapted version of the SORT-seq protocol (Muraro et al. 2016 with primers described in van den Brink et al. 2017). Briefly, after cell lysis, second-strand cDNA synthesis was done, and all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol (Hashimshony et al. 2016)  to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1×75 bp Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles)

value: Subventricular zone

tag: cell type

value: Neural stem cells

tag: Sex

value: male


title: SVZ_3

description: SORTseq


title: KO3_Liver

city: Shanghai

first: Xing

last: Ming

state: Shanghai

address: Huangpu

department: Department of Endocrine and Metabolic Diseases

country: China

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value¡Ü20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation
An index of the reference genome was built and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with ¡°-rna-strandness RF¡± and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r- project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR[8] between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change¡Ý2 were considered differentially expressed genes/transcripts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: liver tissues

extract_protocol:
According to the manufacturer's protocol, total RNA was extracted using a Trizol reagent kit (Invitrogen, Carlsbad, CA, USA). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase-free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA was synthesized by DNA polymerase I, RNase H, dNTP, and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit (Qiagen, Venlo, The Netherlands), end-repaired, A base added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: age

value: 12-week old

value: Bckdhaf/f;RIP-Cre


title: Scar, WTSH, 1

tag: treatment

value: Sham

value: scar


title: KO1_Liver


title: SVZ_1

description: SORTseq


title: Scar, WTSH, 3

tag: disease state


title: MC_1_Colon_555_CD45pos_5p_GEX

tag: patient id

tag: simplified patient_id

tag: steroids at_the_time_of_biopsy

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: Δihfa KDS1 rep1 - IPOD

tag: media

tag: time of_harvest

value: logarithmic phase


title: WT3_Liver

value: Bckdhaf/f


title: SIC_53_Colon_182_CAP_unselect_3p_GEX

value: Colon mucosal biopsy

value: Control - On ICI Therapy

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

tag: rbc depletion_methods

value: ACK Lysis


title: SIC_53_Colon_182_CD45pos_3p_GEX

value: Fresh

tag: dead cell_depletion_method

tag: cd45 positive_selection

tag: chemistry


title: Δhns KDS1 rep1 - ChIP

tag: strain

tag: genotype

value: LB

tag: chip antibody

value: anti-RNA polymerase antibody (NeoClone WP023)


title: WT2_Liver

tag: tissue

value: liver

tag: age


title: AB7091

description: MARSseq

tag: cell type

value: LSK

value: bone marrow


title: NSC_010

description: SORTseq

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for the identification of the Illumina library barcode, cell barcode, and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of Hg19 with BWA (0.7.15) with default parameters. The data was demultiplexed to single-cells as described in Grün et al. 2014. Mapping and generation of count tables were automated using the MapAndGo script (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo).
The data from all samples were loaded in R (version 4.2.0) and processed using the Seurat package (version 4.1.1 – Hao et al. Cell 2021). More specifically, cells with at least 5000 UMI’s per cell and less than 15% mitochondrial gene content were retained for analysis. The dataset was normalized for sequencing depth per cell, log-transformed using a scaling factor of 10,000.
Assembly: mm10
Supplementary files format and content: Comma-separated file
Supplementary files format and content: Tab-separated file

source_name: Hippocampus

growth_protocol: Neural stem cells (NSCs) were purified the hippocampus of 6 week-old Jax C57BL6/J male mice and cultured. Activated NSCs (aNSCs) were cultured as previously described at 37°C/5% CO2 in serum-free media (aNSC media): DMEM/F12 GlutaMax (Invitrogen 10565018) with B27 (1:50, Invitrogen 17504044), penicillin-streptomycin-fungizone (1:100, Invitrogen 15140122), 20 ng/mL FGF-2 and EGF (PeproTech 100-18B and AF-100-15), and 5 µg/mL Heparin (Sigma H3149).

extract_protocol:
Viable single cells were FACS sorted into 384-well plates (Single Cell Discoveries). Each well of a cell capture plate contains a 50 nl droplet of barcoded primers and 10 µl of mineral oil (Sigma M8410). After sorting, plates were immediately spun and placed on dry ice. Plates were stored at -80°C and shipped to Single Cell Discoveries on dry ice, where single-cell RNA sequencing library prep was performed. Cells were heat-lysed at 65°C.
Libraries for each plate were prepared according to an adapted version of the SORT-seq protocol (Muraro et al. 2016 with primers described in van den Brink et al. 2017). Briefly, after cell lysis, second-strand cDNA synthesis was done, and all the barcoded material from one plate was pooled into one library and amplified using in vitro transcription (IVT). Following amplification, library preparation was done following the CEL-Seq2 protocol (Hashimshony et al. 2016)  to prepare a cDNA library for sequencing using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1×75 bp Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles)

treatment_protocol: To generate quiescent NSCs (qNSCs), aNSCs were treated with BMP-4, with FGF-2 and without EGF (qNSC media), using previously described protocols. qNSC media is similar to aNSC media with the exception of the removal of EGF and the addition of 50 ng/mL BMP-4 (Fisher Scientific 5020BP010). After initial induction of quiescence, qNSCs were fed at least once every two days and were considered quiescent after 3 days of qNSC media treatment. For inducing quiescence exit, qNSCs were treated with aNSC media with the addition of 0.5 µg/mL of the BMP-4 antagonist noggin (PeproTech 120-10C) to more reproducibly induce quiescence exit.

value: Hippocampus

value: Neural stem cells

value: 6 week-old

tag: Sex

value: Male

tag: condition

value: multiplexed sample:Activated and 48hrs exit


title: NSC_009

description: SORTseq

value: multiplexed sample:Quiescent and 24hrs exit


title: Δhns KDS1 rep1 - IPOD

tag: media

tag: time of_harvest

value: logarithmic phase


title: SIC_43_RectosigmoidColon_157_CD45pos_3p_GEX

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

tag: channel

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: WT1_Liver

value: 12-week old

value: Bckdhaf/f


title: AAV-GFP rep. 3

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

description: biological replicate

data_processing:
The quality control and pre-processing of the FASTQ files was performed using fastp, a ultra-fast pre-processor that works on quality-filtering, adapter trimming and per-read quality pruning.(Chen et al., 2018)
RNA-Seq data were mapped and quantified using Salmon (version 1.4.0)  (Patro et al., 2017) and aligned to Reference genome assembly GRCm38
Assembly: GRCm38
Supplementary files format and content: gzipped archive of files containing per-sample, transcript-level quantifications given by Salmon. each file contains (in order): a mapping from the transcript ID to the transcript’s legnth, effective length, the transcripts-per-million mappings observed, and the number of reads mapped to the transcript

source_name: adipocyte

extract_protocol:
TRAP was conducted as previously described (Roh et al., 2017). Pieces of frozen epididymal adipose tissue (100mg) were homogenized by dounce (7ml) in homogenization buffer (50mM Tris [pH7.5], 12mM MgCl2, 100mM KCl, 1% NP-40; 100mg/ml cycloheximide, 1mg/ml sodium heparin, 2mM DTT, 0.2units/ml RNasin, 1x Roche Complete EDTA-free protease inhibitor), and incubated on ice for 15 min with vortexing every 5 min. Lysates were centrifuged at 13,000rpm for 10min and the supernatant was collected after removing the top lipid layer. Anti-GFP antibody (5mg/ml, Abcam ab290) was added to the collected supernatant and rotated for 1h at 4°C. Protein G dynabeads washed twice with low-salt wash buffer (50mM Tris [pH7.5], 12mM MgCl2, 100mM KCl, 1% NP-40, 100mg/ml cycloheximide, 2mM DTT) were added to the lysates with antibody and further rotated for 1h at 4°C. The immunoprecipitates were washed three times in high-salt wash buffer (50mM Tris [pH 7.5], 12mM MgCl2, 300mM KCl, 1% NP-40, 100mg/ml cycloheximide, 2mM DTT) on a magnet. After the ﬁnal wash, immunoprecipitates were subjected to RNA extraction using the Qiagen Micro RNeasy kit according to the manufacturer’s instructions.
For RNA-seq library construction, TRAP-isolated RNA (≤100ng) and SVF-derived adipocyte RNA (100ng) were treated with the Ribo-Zero rRNA removal kit (Epicentre, USA) to deplete ribosomal RNA and converted into double-stranded cDNA using NEBNext mRNA Second Strand Synthesis Module (E6111L). cDNA was subsequently segmented and ampliﬁed for 12 cycles by using Nextera XT DNA Library Preparation Kit (Illumina FC-131, USA). Sequencing libraries were analyzed by Qubit and Agilent Bioanalyzer, pooled at a ﬁnal concentration of noon, and sequenced on a HiSeq2500.

value: adipocyte

value: adipocytes differentiated from iWAT SVF of IRF-2D mice

tag: treatment

value: AAV with GFP


title: MC_2_Colon_576_CD45sort_5p_GEX_B

value: Control - Healthy

value: Initial

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: Flow Cytometry (CD235-)

tag: dead cell_depletion_method

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)

tag: chemistry


title: AAV-GFP rep. 2

description: biological replicate

tag: strain

tag: cell type

tag: genotype


title: SIC_43_RectosigmoidColon_157_3p_GEX

tag: tissue


title: WT KDS1 rep1 - ChIP

value: wild type

tag: media

value: LB

tag: chip antibody

value: anti-RNA polymerase antibody (NeoClone WP023)

tag: time of_harvest

value: logarithmic phase


title: Δihfa KDS1 rep1 - INPUT

value: {delta}ihfA


title: AAV-GFP rep. 1

description: biological replicate


title: SIC_43_LeftColon-uninflamed_157_CD45pos_3p_GEX

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

value: CD235 Bead Depletion

value: Annexin-V Bead Depletion

value: Bead Selection (CD45+)


title: KO1_iWAT

source_name: iWAT tissues

value: iWAT

tag: age

value: 12-week old

value: Bckdhaf/f;RIP-Cre


title: WT KDS1 rep2 - INPUT


title: SIC_43_LeftColon-uninflamed_157_3p_GEX

tag: initial vs_follow_up_sample

value: Initial

tag: channel

tag: pcr primer

tag: processed from_fresh_or_frozen_blood

value: Fresh


title: AAV-Cre rep. 3

description: biological replicate

value: adipocyte

value: adipocytes differentiated from iWAT SVF of IRF-2D mice

tag: treatment

value: AAV with Cre


title: SIC_40_Colon_155_CD45pos_3p_GEX

tag: rbc depletion_methods

tag: dead cell_depletion_method

tag: cd45 positive_selection

tag: chemistry


title: WT KDS1 rep2 - IPOD

tag: strain

tag: genotype

value: wild type

tag: media

value: LB


title: Δhns KDS1 rep1 - INPUT

tag: time of_harvest

value: logarithmic phase


title: WT KDS1 rep1 - IPOD


title: WT3_iWAT

tag: tissue

value: Bckdhaf/f


title: SIC_40_Colon_155_3p_GEX

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

tag: disease state


title: AAV-Cre rep. 1

description: biological replicate

tag: cell type


title: WT2_iWAT

tag: age


title: AAV-Cre rep. 2

description: biological replicate


title: WT1_iWAT


title: SIC_36_Colon_140_CD45sort_3p_GEX

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

tag: channel

tag: pcr primer

value: Flow Cytometry (CD235-)

value: Flow Cytometry (DAPI-)

value: Flow Cytometry (CD45+)


title: WT HFD adipocytes mRNA rep. 5

description: biological replicate

value: WT

tag: treatment

value: HFD in thermoneutrality


title: WholeStemR3_Wray_74DAP

city: Urbana

first: Amy

last: Marshall-Colon

state: IL

address: 1201 W Gregory Drive

department: Plant Biology

institute: University of Illinois

description: Internode sections of Wray were cut to 1 cm and flash-frozen in liquid nitrogen. The frozen sections were then embedded in optimal cutting temperature (OCT) compound and placed at -80ºC for 30 minutes to fully solidify. The tissues were mounted by freezing onto magnetic chucks using UltraPure Distilled Water (Invitrogen 10977-015) and 20 μm sections were cut using a cryostat microtome with the following settings: Block temperature -20 ºC and blade temperature -30 ºC. Sections were placed on UV-treated membrane slides and the OCT was removed from the sections by dipping them in a serial dilution (70%, 85%, 100%) of ethanol at 4 ºC for two minutes per dilution. Slides were then allowed to dry for 5 minutes and then either stored at -80 ºC with desiccate or immediately placed on the LCM for sectioning using the following parameters: Energy 56 with delta 27, Focus 67 with delta -2, Cut Speed 20, and Magnification 20x (Blokhina et al., 2017). Working time at room temperature for each slide was no more than two hours. Five cell types (epidermis, pith parenchyma, phloem, xylem parenchyma, and xylem sclerenchyma/xylary fiber cells) were collected separately by catapulting into 0.2 mL tube caps containing 20 μL of RNAqueous Lysis Solution (Thermo AM1912).

data_processing:
Quality check was implemented using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
BBDuk from BBTools suite (https://sourceforge.net/projects/bbmap/) was used to trim raw reads. BBDuk removed adapter sequences from the left end of reads and low-quality bases from both ends until the quality score at the operating base position reached the minimum of 10, and only kept reads with a self-defined minimal length and an average quality score of 10 after the first two trimming steps. The minimal length was defined as the one that reads equal to or longer than this length constitute 95% of total reads so that most of the sequencing information can be retained but sequencing noise introduced by too short reads is removed.
Quality check was implemented after the read trimming process to ensure that trimmed reads have no adapter content and reach the required quality score. Reads verified by FastQC were used for count quantification at the transcript level.
Salmon (Patro et al., 2017) mapping-based mode was used to get transcript count. First, the decoy-aware transcriptome index was generated by concatenating the genome sequence to the end of the transcriptome sequence as described in its supportive alignment guide (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/). Second, the Salmon quantifying method was used to get transcript counts. Transcriptome and genome sequence files used in the indexing process were from Sorghum bicolor v3.1.1 archived on Phytozome (https://data.jgi.doe.gov/refine-download/phytozome). This transcript count profile was used for downstream UMAP visualization, differentially expressed gene (DEG) analysis, Tau (τ) index calculation, and gene regulatory network (GRN) construction, but with different preprocessing and normalization processes.
Assembly: Sorghum bicolor v3.1.1 archived on Phytozome (https://data.jgi.doe.gov/refine-download/phytozome).
Supplementary files format and content: .csv file represents number of raw read counts mapping to each gene

organism: Sorghum bicolor

source_name: whole stem

growth_protocol: Sorghum bicolor cv. Wray was grown in a greenhouse with the 14-h long day and well-watered conditions. Five-gallon pots were used for planting, filled with MetrtoMix900 (SunGro Horticulture, Agawam, MA) and fertilized with 30 g 14-14-14 Osmocote per pot (The Scotts Company, Marysville, OH). Seeds were obtained from the Texas A&M Breeding Program (College Station, TX, USA). Wray stem samples were collected from the most recently fully elongated internode (phytomer 8) of 74-day-old vegetative phase plants. Four biological replicates from four plants were collected, rapidly frozen, and sent on dry ice to Pacific Northwest National Laboratory (PNNL, WA, USA) for the isolation of different stem cell types using LCM, followed by RNA-Seq to achieve the cell-type transcriptomes.

extract_protocol: Full-length cDNA synthesis, fragmentation of synthesized cDNA, and indexing were performed using SMART-Seq® v4 PLUS Kit (cat# R400753) for a RNA-Seq library construction, according to the manufacturer's protocol. Single-end read sequencing with the read length of 150 bp was performed on NextSeq 550 Sequencing System using NextSeq 550 High Output v2 kit 150 cycles (cat#20024907). As a result, cell-type transcriptomes with the total read of 23870982 on average were generated. Bulk RNA-Seq for the whole stem tissue from the same internodes was performed following the same pipeline but without LCM-based target cell type enrichment process. Sequencing for the whole stem tissue generated the average library size of 31538064 reads.

value: Wray


title: WT HFD adipocytes mRNA rep. 6

description: biological replicate


title: KO3_eWAT

source_name: eWAT tissues

value: eWAT

value: 12-week old

value: Bckdhaf/f;RIP-Cre


title: KO2_iWAT

value: iWAT


title: WholeStemR2_Wray_74DAP


title: KO3_iWAT


title: KO2_eWAT


title: SIC_36_Colon_140_CD45pos_3p_GEX

value: Initial

tag: processed from_fresh_or_frozen_blood

value: Fresh

tag: rbc depletion_methods

value: CD235 Bead Depletion

tag: dead cell_depletion_method

value: Annexin-V Bead Depletion

tag: cd45 positive_selection

value: Bead Selection (CD45+)


title: WT HFD adipocytes mRNA rep. 4

description: biological replicate

tag: strain

value: adipocyte

tag: genotype


title: SIC_188

data_processing:
We used Cell Ranger v3.1.0 for generating gene count matrices from sequencing reads (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). We used R scripts to analyze the count matrices.
Assembly: GRCh38-3.0.0
Supplementary files format and content: H5 files, anndata h5ad files, HTML files, CSV files
Supplementary files format and content: Read counts and quality control metrics from Cell Ranger

tag: tissue

value: Colon mucosal biopsy

value: PBMC

value: Control

value: Sample collected at the time of colitis assessment/diagnosis

tag: x10x gex_channel_name

tag: x10x tcr_channel_name

tag: x10x bcr_channel_name

value: Frozen

tag: sample hashing_antibody

tag: pool


title: KO2_Liver

value: liver

tag: age


title: SIC_36_Colon_140_3p_GEX

tag: patient id

tag: simplified patient_id

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

tag: chemistry


title: KO1_eWAT

value: eWAT


title: SIC_186

tag: cell type

tag: processed from_fresh_or_frozen_blood


title: WholeStemR4_Wray_74DAP

tag: strain

value: Wray


title: WT HFD adipocytes mRNA rep. 2

description: biological replicate

tag: genotype

value: WT

tag: treatment

value: HFD in thermoneutrality


title: XylemSclerenchymaR4_Wray_74DAP

source_name: xylem sclerenchyma


title: WT3_eWAT

tag: tissue

value: 12-week old

value: Bckdhaf/f


title: XylemSclerenchymaR3_Wray_74DAP


title: WT2_eWAT


title: XylemSclerenchymaR2_Wray_74DAP


title: WT HFD adipocytes mRNA rep. 1

description: biological replicate


title: IRF3-KO HFD adipocytes mRNA rep. 6

description: biological replicate

value: adipocyte IRF3KO


title: VascularParenchymaR4_Wray_74DAP

source_name: vascular parenchyma


title: WT1_eWAT


title: SIC_134

tag: x10x gex_channel_name

tag: x10x tcr_channel_name


title: SIC_126

tag: x10x bcr_channel_name

tag: sample hashing_antibody


title: SIC_109

tag: pool


title: PhloemR4_Wray_74DAP

source_name: phloem


title: Dataset D10 lib7

city: New York City

first: Itai

last: Yanai

state: NY

address: 435 East 30th Street

institute: NYU Langone Health

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib7

data_processing:
All analysis was performed using the Tavazoie lab computational pipeline (https://tavazoielab.c2b2.columbia.edu/PETRI-seq/PETRI_Seq_Computational.pdf).
Initial QC was performed using FastQC then unique molecular identifiers were extracted with UMI tools. Initial demultiplexing by cell barcode was performed iteratively using Cutadapt.
After selecting barcodes associated with the highest number of reads, reads from individual barcodes were aligned to the E. coli MG1655 or B. subtilis 168 reference genome using BWA.
Numbers of reads mapping to individual genes were quantified using FeatureCounts before counts were collapsed into unique reads based on UMI and used to make the final counts matrix.
Sample annotations were extracted from the number of barcode 1, since this corresponds to the way samples were added in the initial plate during reverse transcription.
Assembly: E. coli reads were aligned to the K-12 MG1655 reference assembly (GCA_000005845.2). B. subtilis reads were aligned to the 168 reference assembly (GCF_000009045.1).
Supplementary files format and content: Counts matrices: gzip-compressed tab-separated text files of counts by genes (columns) by cell barcode (rows) ("_counts.txt.gz")
Supplementary files format and content: Metadata files: tab-separated files containing library and sample information for each cell barcode ("_metadata.txt").

organism: Escherichia coli

source_name: Whole bacteria

growth_protocol: Bacteria were streaked out onto agar from frozen stocks overnight then grown overnight in LB. Samples were then diluted back to grow in the medium and to the densities indicated. There was an initial "back-dilution" step prior to harvesting to improve population homogeneity.

extract_protocol:
Samples were fixed and processed according to the protocol of Blattman et al. (PMID: 32451472). Briefly, cells were fixed overnight with 4% formaldehyde, permeabilized with 50% ethanol followed by enzymatic cell wall digestion (100 µg/ml lysozyme, 15 min), then treated with DNase to remove genomic DNA.
Reverse transcription and split-pool barcode ligation were carried out in situ in fixed cells according to the protocol of  Blattman et al. (PMID: 32451472). After barcoding, cells were separated into aliquots of ~20,000 cells for further processing. After lysis and reversal of crosslinking, second strand synthesis was performed using the NebNext Second Strand Synthesis module (New England Biolabs) and tagmentation was carried out using the EZ-Tn5 transposase (Lucigen), before final amplification with multiplex indexing primers.

treatment_protocol: B. subtilis cells were not subject to further treatment besides growth. For E. coli, cells were either harvested in balanced growth or after 1:1 dilution into 2x LB medium.

value: Whole bacteria

tag: cell line

value: Bacteria

value: LB and/or M9 + Glc + AA


title: WholeStemR1_Wray_74DAP


title: IRF3-KO HFD adipocytes mRNA rep. 4

description: biological replicate

value: adipocyte


title: Dataset D10 lib5

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib5


title: IRF3-KO HFD adipocytes mRNA rep. 1

description: biological replicate


title: Dataset D10 lib6

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib6


title: XylemSclerenchymaR1_Wray_74DAP


title: SIC_140_Colon_441_CD45sort_5p_GEX

value: Colon mucosal biopsy

tag: patient id

tag: simplified patient_id

value: Initial

tag: channel

tag: pcr primer

tag: rbc depletion_methods

value: Flow Cytometry (CD235-)

tag: dead cell_depletion_method

value: Flow Cytometry (DAPI-)

tag: cd45 positive_selection

value: Flow Cytometry (CD45+)


title: VascularParenchymaR2_Wray_74DAP

tag: strain


title: SIC_141

tag: cell type

value: PBMC

tag: disease state

value: irColitis Case

tag: steroids at_the_time_of_biopsy

value: Prednisone 3 mg

tag: initial vs_follow_up_sample

value: Sample collected at the time of colitis assessment/diagnosis

tag: processed from_fresh_or_frozen_blood

value: Frozen


title: IRF3-KO HFD adipocytes mRNA rep. 5

description: biological replicate

tag: genotype

tag: treatment

value: HFD in thermoneutrality


title: WT HFD adipocytes mRNA rep. 3

description: biological replicate

value: WT


title: Dataset D10 lib8

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib8

tag: tissue


title: Dataset D10 lib3

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib3

tag: cell line


title: SIC_172

tag: patient id

value: Control

tag: x10x gex_channel_name

tag: x10x tcr_channel_name

tag: x10x bcr_channel_name

tag: sample hashing_antibody

tag: pool


title: IRF3-KO HFD adipocytes mRNA rep. 3

description: biological replicate

value: adipocyte IRF3KO


title: SIC_100

tag: simplified patient_id

value: Prednisone (stopped 6 weeks before biopsy)


title: OB015_SVF_PD1_PLUS

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.32)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts. Only reads mapped to exons were considered in the counting procedure.
Genomic features were annotated according to the Gencode basic annotations (Gencode version 28)
Assembly: UCSC hg38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: stromal vascular fraction

extract_protocol:
RNA extraction was carried out with Qiagen Micro RNeasy kit
cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan)

treatment_protocol: Peripheral blood samples were processed to isolate PBMC using Lympholyte Cell Separation density gradient centrifugation media . Visceral adipose tissue samples were minced and enzimatically digested to isolate stromal vascular fraction (SVF). PBMC and SVF samples were FACS-stained to sort PD-1+ CD4 Tconv cells

value: stromal vascular fraction

tag: cell subset

value: PD-1+ CD4 Tconv cells

value: primary CD4 T lymphocytes

value: obese dysglycemic

tag: patient of_origin


title: IRF3-KO HFD adipocytes mRNA rep. 2

description: biological replicate

tag: strain

tag: cell type

value: adipocyte


title: SIC_140

value: Colon mucosal biopsy

tag: disease state

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample


title: Dataset D10 lib4

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib4

value: Whole bacteria

value: Bacteria

tag: genotype

tag: treatment

value: LB and/or M9 + Glc + AA


title: PhloemR3_Wray_74DAP

value: Wray


title: VascularParenchymaR1_Wray_74DAP


title: VascularParenchymaR3_Wray_74DAP


title: SIC_97

tag: tissue

value: PBMC

value: irColitis Case

value: Sample collected at the time of colitis assessment/diagnosis

tag: processed from_fresh_or_frozen_blood


title: SIC_100.1

tag: patient id

value: Follow up timepoint after colitis resolution

tag: x10x gex_channel_name

value: Frozen


title: Dataset D10 lib2

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib2

tag: cell line

value: WT


title: PhloemR2_Wray_74DAP


title: SIC_94

value: Control

tag: x10x tcr_channel_name

tag: x10x bcr_channel_name

tag: sample hashing_antibody


title: OB010_SVF_PD1_PLUS

value: stromal vascular fraction

tag: cell subset


title: SIC_89

tag: simplified patient_id

value: Prednisone 2.5 mg

tag: pool


title: PithParenchymaR4_Wray_74DAP

source_name: pith parenchyma

tag: strain


title: PithParenchymaR3_Wray_74DAP


title: SIC_71

tag: cell type

tag: disease state


title: Spl_KO_3

city: Erlangen

first: Hans-Martin

last: Jäck

address: Glückstrasse 6

department: Molecular Immunology

country: Germany

institute: Universitätsklinikum Erlangen

data_processing:
Sequenced reads were trimmed for adaptor sequences and mapped to the GRCm38 mouse genome with STAR 2.6.1
Gene-wise counts were generated with salmon 1.4.0
Supplementary files format and content: Combined table with summarized gene-wise counts for each sample

source_name: Spleen

extract_protocol:
Splenic plasma cells were FACS-purified (CD138+ TACI+) and sorted directly into beta-mercaptoethanol-containing RLT (Qiagen) Lysis buffer. Total RNA was isolated with the RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed with the Takara Clontech Smart-Seq v4 Low input kit according to manufacturers instructions and sequenced on Illumina Hiseq X instruments.

value: Spleen

value: plasma cell


title: Spl_KO_2


title: OB005_SVF_PD1_PLUS

value: PD-1+ CD4 Tconv cells

value: primary CD4 T lymphocytes

value: obese normoglycemic

tag: patient of_origin


title: Spl_Cre_3

tag: genotype


title: OB018_SVF_PD1_PLUS


title: PithParenchymaR2_Wray_74DAP


title: OB013_SVF_PD1_PLUS


title: PhloemR1_Wray_74DAP


title: Spl_Cre_4


title: SIC_43

value: Colon mucosal biopsy

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample


title: OB023_PBMC_PD1_PLUS

source_name: peripheral blood

tag: tissue

value: peripheral blood

value: obese dysglycemic


title: PithParenchymaR1_Wray_74DAP

value: Wray


title: Spl_Cre_2


title: OB015_PBMC_PD1_PLUS


title: SIC_40

source_name: Colon mucosal biopsy

value: PBMC

tag: patient id

value: irColitis Case

tag: processed from_fresh_or_frozen_blood


title: Dataset D10 lib1

description:
E. coli grown in M9GA or LB/M9GA mix, either in balanced growth or after shift to higher growth rate
D10 lib1

value: Whole bacteria

tag: cell line

value: Bacteria

tag: treatment

value: LB and/or M9 + Glc + AA


title: OB001_SVF_PD1_PLUS


title: Spl_Cre_1


title: OB010_PBMC_PD1_PLUS


title: EpidermisR3_Wray_74DAP

source_name: epidermis


title: EpidermisR4_Wray_74DAP


title: SIC_36

value: Sample collected at the time of colitis assessment/diagnosis

tag: x10x gex_channel_name

tag: x10x tcr_channel_name

tag: x10x bcr_channel_name

value: Frozen


title: Spl_KO_1


title: SIC_32

tag: simplified patient_id

tag: sample hashing_antibody


title: OB001_PBMC_PD1_PLUS

tag: cell subset


title: SIC_43.1

tag: cell type

value: Follow up timepoint after colitis resolution

tag: pool


title: EpidermisR2_Wray_74DAP

tag: strain


title: SIC_31

tag: disease state

value: Control


title: OB018_PBMC_PD1_PLUS

tag: patient of_origin


title: EpidermisR1_Wray_74DAP


title: WGBS, Cdca7G305V/G305V, rep2

city: Leiden

first: Lucia

last: Daxinger

address: Albinusdreef 2

country: Netherlands

institute: Leiden Univeristy Medica Center

data_processing:
Raw sequences were filtered by quality with TrimGalore using default parameters. Reads with length smaller than 20 bps and error rate higher than 0.1 were discarded. Sequences were aligned to mm10 (transgene sequence was included into mm10 FASTA file) using the Bismark aligner v0.18 (Krueger and Andrews, 2011). To increase sensitivity we used parameter “-N 1”, as well as –gzip –bowtie2. The duplicates in the alignment were removed with Deduplicate Bismark (part of the Bismark package)
Methylation calling was performed by Bismark Methylation Extractor (part of the Bismark package), using default parameters with the following exceptions: “–paired-end”, “–ignore_r2 2” and  “–bedgraph”. Correlation was calculated and plots were made using the Methylkit R package. Differentially methylated CpGs were calculated using DSS R package v2.3 (ref Park Y, Wu H (2016).)
bigWig files were generated using deepTools version 3.1.3 (Ramirez et al., 2016). Score represents the normalized coverage of DNA fragments at a given genomic coordinate
Assembly: mm10
Supplementary files format and content: bigWig, differentially methylated CpGs (DMLs)

extract_protocol: Genomic DNA (gDNA) was isolated using the salt-extraction method. Briefly, tissues were lysed in cell lysis buffer (50 mM Tris-HCl (pH 8), 4 mM EDTA (pH 8), 2% SDS) plus Proteinase K (390973P; VWR), and incubated at 55°C overnight. Cell lysate was treated with RNaseA (EN0531; Thermo) at 37°C for 1 h. Saturated NaCl buffer was added followed by addition of isopropanol to precipitate gDNA and washing with 70% EtOH. Genomic DNA was dissolved in water and concentration was measured using Nanodrop.

value: Spleen

value: FVB

tag: age

tag: genotype


title: OB013_PBMC_PD1_PLUS

tag: tissue

value: PD-1+ CD4 Tconv cells

value: primary CD4 T lymphocytes


title: WGBS, Cdca7G305V/G305V, rep1


title: SIC_19

value: Colon mucosal biopsy

tag: patient id

tag: steroids at_the_time_of_biopsy

tag: initial vs_follow_up_sample

tag: processed from_fresh_or_frozen_blood


title: SIC_13

tag: x10x gex_channel_name

tag: x10x tcr_channel_name


title: Developing_Biolrep_4

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
Raw counts were obtained with kallisto.
Assembly: GCA_028583425.1
Supplementary files format and content: Raw counts in a tab delineated matrix.

organism: Eublepharis macularius

source_name: developing teeth

extract_protocol:
Each sample contained developing or functional teeth samples . Tubes were snap frozen in liquid nitrogen. Each sample was disrupted using a glass tissue grinder and a Qiagen Shredder column (ID:79656). Total RNA was extracted using a Qiagen RNeasy micro kit (ID: 74004).
Qualifying samples were prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs) at Biomedical research Center sequencing Core at University of British Columbia. Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads. Sequencing data was demultiplexed using Illumina's bcl2fastq2. The output was 20 million paired end reads

value: developing teeth

tag: Sex

value: male

tag: developmental stage

value: adult

tag: rin number

tag: number of_teeth_per_sample


title: Functional_Biolrep_4

source_name: functional teeth

value: functional teeth


title: MC_2

tag: cell type

value: PBMC

tag: simplified patient_id

tag: x10x bcr_channel_name

tag: sample hashing_antibody

tag: pool


title: WNTd-HE CD34+CD43-CD184-CD73-cells [scRNA-seq]

first: Monah

last: Abou Alezz

address: Via Olgettina 60

institute: SR-TIGET

data_processing:
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvain algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Seurat
Assembly: GRCh38
Supplementary files format and content: Sparse Cellranger matrix

source_name: H1 human embryonic stem cells

growth_protocol: H1 human embryonic stem cells were expanded and differentiated as reported in Ditadi et al., 2015 (doi.org/10.1038/ncb3161); Ditadi et al, 2016 (doi.org/10.1016/j.ymeth.2015.10.001)

extract_protocol:
On day 8 of culture, embryoid bodies were dissociated with 0.25% Trypsin-EDTA for 8 minutes and Collagenase II for 30 minutes, immunolabled at 4C for 25 minutes. CD34+CD43–CXCR4–CD73– hemogenic endothelial cells were then FACS sorted using a BD FACSMelody and stored on ice until ready for library preparation.
scRNA-Seq libraries were prepared according to the manufacturer’s instructions

value: isolated cells of Wnt dependent hematopoietic culture

tag: time

value: Day 8


title: OB005_PBMC_PD1_PLUS

tag: tissue

value: peripheral blood

tag: cell subset

tag: disease state

value: obese normoglycemic

tag: patient of_origin


title: WGBS, WT, rep2

tag: strain

tag: age

tag: genotype


title: WGBS, WT, rep1


title: PD17 D14

status: Public on Feb 08 2024

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

data_processing:
Initial bioinformatics analysis were conducted by GENEWIZ. Sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality (Trimmomatic v.0.36). Using the STAR aligner v.2.5.2b the trimmed reads were mapped to the Homo sapiens GRCh38 reference. genome available on ENSEMBL.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: tab-delimited text files include count values for each sample

extract_protocol:
High Pure RNA Isolation Kit (Roche) was used for RNA extraction from cultured cells. Total RNA from the wild-type and GLI2mut heterozygous  iPSC cells at d0, gut tube (D5) and endocrine progenitor (D14) stage of pancreatic differentiation (PD) were extracted from two independent biological replicates. Total RNA concentration and RNA integrity of each sample were determined with NanoDrop and Qubit 4 Fluorometer.
RNA library preparations and sequencing reactions were conducted by the company GENEWIZ using standard Illumina protocols. Briefly, data was generated with an Illumina HiSeq 2x150 PE HO configuration.

treatment_protocol: iPSC cells were differentiated along pancreatic cell lineage using the Russ et al protocol (Embo J 2015, 34(13):1759-72).

tag: cell line

value: iPSC

value: wild-type

tag: treatment

value: D14 endocrine differentiation stage


title: PD17 D14 het

value: GLI2mut heterozygous


title: PD17 D5

value: D5 gut tube differentiation stage


title: PD17 D5 het


title: PD17 D0

value: untreated


title: PD17 D0 het


title: PD15 D14 het


title: PD15 D5


title: PD15 D5 het


title: PD15 D0 het


title: des trunk group 3

city: Umeå

first: Nils

last: Dennhag

address: Linneaus väg 9

country: Sweden

institute: Umeå Univeristy

data_processing:
Sequence reads were mapped to GRCz11 using STAR (options: --outSAMtype BAM SortedByCoordinate --seedSearchStartLmax 12 --outFilterScoreMinOverLread 0.3 --alignSJoverhangMin 15 --outFilterMismatchNmax 33 --outFilterMatchNminOverLread 0 --outFilterType BySJout --outSAMunmapped Within --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantMode GeneCounts)
Read count extraction and normalization were performed using R package DeSEQ2
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts

organism: Danio rerio

source_name: trunk muscle

growth_protocol: WT AB zebrafish used originated from the same line utilized when generating the desma-/-;desmb-/- double mutant. Zebrafish were maintained by standard procedures on a 10/14h dark/light cycle at 28°C

extract_protocol:
Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA-later solution from Sigma and stored at -80C. All collected samples were then treated with TRIZOL according to the manufactors description. 400ng total RNA was used for library construction.
Illumina TruSeq Stranded mRNA, poly-A selection

value: trunk muscle

value: 5 month old

value: AB

value: Trunk muscle myofibers

value: desma-/-;desmb-/-


title: PD15 D0


title: des trunk group 2


title: des trunk group 1


title: des EOM group 2

source_name: extraocular muscle

value: extraocular muscle

value: extraocular myofibers


title: des EOM group 1


title: wt EOM group 1

value: WT


title: sibCGFP4

source_name: 5 dpf trunk

value: 5 dpf trunk

value: zebrafish trunk


title: des EOM group 3


title: wt trunk group 1


title: wt trunk group 2


title: sibCGFP3


title: wt EOM group 3


title: sibCGFP2


title: sibC3

value: dmd+/-


title: sibCGFP1


title: wt EOM group 2


title: sibC4


title: dmdGFP2


title: dmdGFP4


title: sibC1


title: PD15 D14

value: iPSC


title: dmdGFP3


title: sibC2


title: dmdGFP1


title: dmd3

value: dmd-/-


title: dmd2


title: dmd4


title: dmd1


title: wt trunk group 3


title: 20m des trunk group 2

source_name: 20 month old trunk muscle

extract_protocol:
Muscle tissue was dissected from freshly sacrificed zebrafish and dissected in RNA-later solution from Sigma and stored at -80C. All collected samples were then treated with TRIZOL according to the manufactors description. 200ng total RNA was used for library construction.
Illumina TruSeq Stranded mRNA, poly-A selection

value: 20 month old


title: 20m des trunk group 1


title: 20m wt trunk group 3


title: 20m wt trunk group 2


title: 20m wt trunk group 1


title: 20m des EOM group 2

source_name: 20 month old extraocular muscle


title: 20m des EOM group 1


title: 20m wt EOM group 3


title: 20m des EOM group 3


title: 20m wt EOM group 2


title: MCF10A cells (miR-708, BR9)

city: New Haven

first: Carson

last: Bryant

state: CT

address: 333 Cedar Street

department: Molecular Biophysics and Biochemistry

institute: Yale University

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt

data_processing:
Adapters were trimmed using CutAdapat 1.12 with default parameters.
Trimmed reads were aligned to the hg38 genome assembly using HISAT 2.1.0 with default parameters.
Aligned reads were quantified with the RefSeq Transcripts 93 annotation using the Partek Flow E/M (expectation maximization) script with default parameters.
Quantified reads were subjected to differential expression analysis using the Partek Flow implementation of DESeq2 with default parameters.
Assembly: hg38
Supplementary files format and content: counts.txt: DESeq2 normalized read counts for indicated cell line samples.
Supplementary files format and content: gsa_result.txt: DESeq2 differential expression quantification/statistics for indicated cell line samples.

growth_protocol: Cells were seeded at a density of 100,000 cells/well in 6-well plates and grown in appropriate medium.

extract_protocol:
RNA was harvested using TRIzol according to the manufacturer's instructions.
The Yale Center for Genomic Analysis synthesized the PolyA+ mRNA library following Illumina mRNA sample preparation guidelines and also performed paired-end RNA sequencing using the Illumina HiSeq/NovaSeq sequencing system.

treatment_protocol: Cells were treated for 72 h with 30 nM non-targeting siRNA (siNT) or MIR-28 microRNA mimics (hsa-miR-28-5p or hsa-miR-708-5p) from Dharmacon/Horizon Discovery.

value: breast epithelial cells


title: 20m wt EOM group 1


title: MCF10A cells (siNT, BR9)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt

value: siNT


title: MCF10A cells (siNT, BR7)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: MCF10A cells (miR-28, BR7)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: MCF10A cells (siNT, BR8)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: MCF10A cells (miR-28, BR8)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: MCF10A cells (miR-708, BR8)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: MDA_23-4_S9

city: Paris

first: Benjamin

last: SAINTPIERRE

address: 22 Rue Mechain

country: France

institute: Inserm

data_processing:
STAR  --genomeDir /path/to/STAR/reference/directory  --sjdbGTFfile /path/to/gtf --runThreadN 20  --readFilesIn /path/to/fastq/R1 /path/to/fastq/R2  --outFileNamePrefix $echantillon  --twopassMode Basic  --sjdbOverhang 74  --outSAMtype BAM SortedByCoordinate  --readFilesCommand zcat  --outSAMunmapped Within  --outFilterType BySJout  --quantMode TranscriptomeSAM
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output /path/to/AlignedToTranscriptome/file /path/to/rsem-prepare-reference/files [sample-rsem-suffix]
Assembly: Ensembl release 101, Homo sapiens GRCh38
Supplementary files format and content: RSEM raw count matrix

source_name: breast

growth_protocol: The cell lines were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, Illkirch, France), supplemented with 10% FCS and 1% penicillin-streptomycin. The cultures were maintained at 37°C in a humidified 5% CO2 / 95% air incubator until the cells reached 80% confluence. They were then harvested by trypsinization and centrifugated at 500 xg for 10 minutes.

extract_protocol: RNA was extracted from the breast cancer cells with QIAGEN RNeasy® Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction.

value: breast


title: MDA-CS_29-3_S11

value: exposition to umbilical cord blood CD34+ cells


title: 20m des trunk group 3

value: trunk muscle


title: MDA-CS_19-2_S10


title: MDA_19-2_S7


title: MDA-CS_23-4_S12


title: MCF-CS_19-2_S4


title: MDA_29-3_S8


title: MCF-CS_23-4_S6


title: MCF-CS_29-3_S5


title: MCF10A cells (miR-708, BR7)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: MCF_19-2_S1


title: CDK12.CHIP_2

city: Guangzhou

first: Jingting

last: Li

address: No 1, Zhongshan 2 Road, 12th Floor

department: Institue of Precision Medicine

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

description:
ChIP-Seq
CDK12.CHIP2.bed

data_processing:
Raw ChIP-seq reads were aligned using Bowtie v2.3.
MACS2 (version 2.2.4) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped among all replicates were obtained using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks

source_name: Human epidermal keratinocyte

growth_protocol: Primary keratinocytes were grown on culture dishes in keratinocyte EPILIFE medium (Life technologies).

extract_protocol:
10 million cells were crosslinked with 2mM DSG and 1% formaldehyde in the experiment. The ChIP experiment was done using the Lab ChIP-seq protocol, DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: CDK12 siRNA knockdown and induced to differentiation by 1.2mM calcium

tag: timepoints

value: 3 days

value: Ca2+ induced differentiation for 3 days


title: MCF_23-4_S3


title: MCF_29-3_S2


title: Pooled_input_CDK12.CHIP

description: ChIP-Seq


title: MCF10A cells (miR-28, BR9)

description:
counts_MCF10A.txt
gsa_result_MCF10A.txt


title: CDK12.CHIP_1

description:
ChIP-Seq
CDK12.CHIP1.bed


title: CTLi.Ser2CHIP_replicate2

description:
ChIP-Seq
CTLi.Ser2CHIPseq.bed

tag: antibody


title: Pooled_input_Ser2CHIP

description: ChIP-Seq


title: OVX_6

city: Chicago

first: Priyam

last: Patel

address: 750 North Lake Shore Drive, Rubloff 11-146

department: Quantitative Data Science Core

institute: Northwestern University

data_processing:
Trim Galore
Adapters were trimmed, and reads that were either of poor quality or aligned to rRNA sequences were filtered using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The cleaned reads were then aligned to the mouse genome (mm10) using STAR. Read counts for each gene were computed using HTSeq-Counts, in conjunction with a gene annotation file for mm10 obtained from Ensembl (http://useast.ensembl.org/index.html). A comprehensive quality control report was assembled using MultiQC
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from the dorsal cerebral cortex using Trizol reagent, as per the protocol by Dodiya et al. [9], and cleaned with the RNAeasy Micro kit (Qiagen).
RNA-seq library preparations and sequencing were performed using an Illumina HiSeq4000 at The University of Chicago Genomics Core Facility.

value: cerebral cortex

tag: cell type

value: Ovariectomy surgery


title: CTLi.Ser2CHIP_replicate1

description:
ChIP-Seq
CTLi.Ser2CHIPseq.bed


title: OVX_3


title: OVX_4


title: OVX_5


title: Sham_4

value: Sham


title: OVX_2


title: Sham_1


title: Sham_5


title: Sham_2


title: Sham_6


title: OVX_1


title: Sham_3


title: TKO4

first: Shujia

last: Lin

address: No. 355 Luding Road, Shanghai, China

institute: Shanghai Children’s Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.6.1p2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (v1.26.0). Pvalue < 0.05 and absolute log2 (fold change) > 0.58 were set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: Heart

extract_protocol:
Hearts were removed, flash fronzen in liquid nitrogen and RNA was extracted using Trizol reagant.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.

tag: srain

value: heart

tag: gender

value: female

value: TECRL-/-


title: TKO2


title: S4


title: TKO1


title: TKO3


title: S5


title: TKO5

value: male


title: TKO6


title: CDK12i.Ser2CHIP_replicate2

description:
ChIP-Seq
CDK12i.Ser2CHIPseq.bed


title: S6


title: CDK12i.Ser2CHIP_replicate1

description:
ChIP-Seq
CDK12i.Ser2CHIPseq.bed


title: S2

value: wild type


title: S3


title: S12


title: S10


title: S8


title: S9


title: WT2


title: S7


title: WT1


title: Pm1, 191010, CA

city: Bethesda

first: Ousmane

middle: Hamadoun

last: Cisse

state: MD

address: 10 Center Dr,

institute: National Institutes of Health

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Hiseq X  output.
To remove mouse DNA, ChIP-seq reads were aligned to the mouse genome (GCF_000001635.25)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
ChIP-seq reads were aligned to the Pneumocystis murina genome using bwa mem version 0.7.17-r1188
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.05 (narrowPeak files)
bigWig files were generated using the bamCoverage from deepTools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate (bins per millions; bin size; 50 bp)
Assembly: GCF_000349005.1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Pneumocystis murina

source_name: lungs

extract_protocol:
Cells were fixed with formaldehyde for 10 minutes using the active motif Low cell ChIP-seq (cat # 53084). After quenching and cell lysis, chromatin was sonicated using a Q800R3 Sonicator (Qsonica) with recirculating chiller.
ChIP-seq libraries were prepared using the active motif Low cell ChIP-seq (cat # 53084) that include the Next Gen DNA library kit and Next Gen Indexing kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 14 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRIselect  beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: lungs

value: mouse C1 seeder

value: infection level 5+

value: collect date:10/10/19

tag: chip antibody

value: CENP-A (Genescript #1598083)


title: Pm1, 191010, CP

value: pre immune serum


title: Pm, 211220, S22

source_name: coculture day 10

value: coculture day 10

value: Pneumocystis + epithelial cell lines

value: collect date:12/07/21

value: H3K9me3 (Abcam # ab8898)


title: S1


title: Pm, 211220, S23

value: H3K4me2 (Abcam # ab8580)


title: Pm, 211220, S20 (input)


title: Pm, 211220, S19


title: S11


title: Pm, 211220, S21

value: H3K9me2 (Abcam # ab1220)


title: Pneumocystis murina, coculture A549/LET1, day 7

data_processing:
Sequences were trimmed for adaptor sequence/low-quality sequence using cutadapt
To remove mouse DNA, RNA-seq reads were aligned to the mouse genome (GCF_000001635.25)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
Reads were aligned to Pneumocystis murina genome using star v.2.7.9a
Read count and normalization were performed using deepTools
Assembly: GCF_000349005.1
Supplementary files format and content: bigWig

source_name: partially purified cell pellet

growth_protocol: Pneumocystis murina coculture

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq library Prep kit following manufacturer’s instruction.

treatment_protocol: no treatement

value: partially purified cell pellet

value: coculture with A549/LET1

value: Fungus/mammalian epithelial cells


title: Pneumocystis murina, coculture A549/LET1, day 14


title: Pneumocystis murina, coculture A549/LET1, day 0

source_name: partially purified cell pellet from infected mice lungs


title: PB02001_2_tumor_roi001_Fibrosis

type: protein

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: protein detected by antibody

hyb_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

data_processing: Raw count data of antibody-captured protein copy numbers in each segment were normalized by scaling with geometric mean of the counts of the housekeeping proteins

label: fluorescent barcode

molecule: protein

treatment_protocol: Pre-treatment tumor and liver biopsy tissues were obtained from patients with unresectable hepatocellular carcinoma trated with bavituximab and pembrolizumab.

tag: patient id

tag: tissue type

value: tumor

tag: region of interest (roi) number

tag: segment type

value: fibrous tissue enriched

tag: positive immuno-fluorescent morphology marker

value: SMA

tag: radiographic objective response

value: stable disease (SD)


title: PB02001_2_tumor_roi001_ImmuneCell

description: protein detected by antibody

scan_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals

value: immune cell enriched


title: PB02001_2_tumor_roi003_Fibrosis

description: protein detected by antibody

label_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: PB02001_2_tumor_roi002_ImmuneCell

description: protein detected by antibody

extract_protocol: Refer to the NanoString Digital Spatial Profiling (DSP) GeoMx analysis manuals


title: PB02001_2_tumor_roi003_CancerCell

description: protein detected by antibody

value: cancer cell enriched


title: PB01015_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB01015_tumor_roi003_CancerCell

description: protein detected by antibody


title: PB02001_2_tumor_roi002_CancerCell

description: protein detected by antibody


title: PB02001_2_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB01015_tumor_roi002_CancerCell

description: protein detected by antibody


title: Pm1, 191010, CC

tag: tissue

value: lungs

value: mouse C1 seeder

value: infection level 5+

value: collect date:10/10/19

value: CENP-C (Genescript # 1525058 )


title: PB01015_tumor_roi002_Fibrosis

description: protein detected by antibody


title: PB01015_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: PB01015_tumor_roi001_CancerCell

description: protein detected by antibody


title: PB01015_tumor_roi001_Fibrosis

description: protein detected by antibody


title: PB02022_tumor_roi003_ImmuneCell

description: protein detected by antibody

value: partial response (PR)


title: PB02022_tumor_roi003_Fibrosis

description: protein detected by antibody


title: PB02001_2_tumor_roi001_CancerCell

description: protein detected by antibody


title: PB01015_tumor_roi003_Fibrosis

description: protein detected by antibody


title: PB02001_2_tumor_roi002_Fibrosis

description: protein detected by antibody


title: PB02022_tumor_roi002_CancerCell

description: protein detected by antibody


title: PB02022_tumor_roi001_CancerCell

description: protein detected by antibody


title: PB02022_tumor_roi003_PanCK_T

description: protein detected by antibody

value: PanCK


title: PB02022_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB02022_tumor_roi002_Fibrosis

description: protein detected by antibody


title: PB02022_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: PB02025_liver_roi005_Fibrosis

description: protein detected by antibody

value: liver

value: progressive disease (PD)


title: PB01015_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB02025_tumor_roi002_CancerCell

description: protein detected by antibody


title: PB02025_liver_roi005_BileDuct

description: protein detected by antibody

value: bile duct


title: PB02025_tumor_roi004_ImmuneCell

description: protein detected by antibody


title: PB02025_liver_roi005_nonTumorLiver

description: protein detected by antibody

value: non-tumor liver


title: PB02022_tumor_roi001_Fibrosis

description: protein detected by antibody

value: tumor


title: PB02025_tumor_roi003_CancerCell

description: protein detected by antibody


title: PB02025_tumor_roi004_Fibrosis

description: protein detected by antibody

value: fibrous tissue enriched


title: PB02025_liver_roi005_ImmuneCell

description: protein detected by antibody


title: PB02025_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB02025_tumor_roi003_Fibrosis

description: protein detected by antibody

value: SMA


title: PB02025_tumor_roi002_Fibrosis

description: protein detected by antibody


title: PB02019_tumor_roi006_ImmuneCell

description: protein detected by antibody


title: PB02019_tumor_roi006_Rest_F

description: protein detected by antibody


title: PB02019_liver_roi005_ImmuneCell

description: protein detected by antibody


title: PB02019_liver_roi005_nonTumorLiver

description: protein detected by antibody


title: PB02025_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: PB02019_tumor_roi004_ImmuneCell

description: protein detected by antibody


title: PB02025_tumor_roi001_CancerCell

description: protein detected by antibody


title: PB02025_tumor_roi001_Fibrosis

description: protein detected by antibody


title: PB02025_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB02019_tumor_roi002_CancerCell

description: protein detected by antibody


title: PB02019_tumor_roi004_PanCK_T

description: protein detected by antibody


title: PB02019_liver_roi005_Fibrosis

description: protein detected by antibody


title: PB02019_tumor_roi004_Fibrosis

description: protein detected by antibody


title: PB02019_tumor_roi003_Fibrosis

description: protein detected by antibody


title: PB02019_liver_roi005_BileDuct

description: protein detected by antibody


title: PB02019_tumor_roi003_CancerCell

description: protein detected by antibody


title: PB02019_tumor_roi001_CancerCell

description: protein detected by antibody


title: PB02019_tumor_roi002_Fibrosis

description: protein detected by antibody


title: PB02019_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: PB02019_tumor_roi001_Fibrosis

description: protein detected by antibody


title: PB02018_liver_roi004_nonTumorLiver

description: protein detected by antibody

value: complete response (CR)


title: PB02019_tumor_roi006_SMA_T

description: protein detected by antibody


title: PB02019_tumor_roi001_ImmuneCell

description: protein detected by antibody

value: immune cell enriched


title: PB02018_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB02018_liver_roi004_Fibrosis

description: protein detected by antibody


title: PB02019_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB02018_liver_roi004_BileDuct

description: protein detected by antibody


title: PB02018_liver_roi004_ImmuneCell

description: protein detected by antibody


title: PB02018_tumor_roi002_Fibrosis

description: protein detected by antibody


title: PB02018_tumor_roi003_CancerCell

description: protein detected by antibody

value: cancer cell enriched


title: PB02018_tumor_roi002_CancerCell

description: protein detected by antibody


title: DX-BLN-072

city: Berlin

first: Luis

middle: Philipp

last: Kuschel

address: Robert-Koch-Platz 4

department: Abteilung für experimentelle Neurologie

institute: Charité Universitätsmedizin Berlin

description:
DX-BLN-072-T01A-D01A-W01
Oxford Nanopore Technologies MinION Mk 1B

data_processing:
*library strategy: nanopore whole genome sequencing
Basecalling was performed using guppy (Oxford Nanopore Technologies, UK) v5.0.16 (CPU-based, fast mode)
Alignment to the hg19 human reference genome using minimap2 v.2.15
Methylation status of CpG sites (5mC) was called using nanopolish v0.11.1 and binarized using a threshold of 0.6
Assembly: hg19
Supplementary files format and content: .bed.txt-files; 5Mc methylation data

source_name: brain tumor tissue

extract_protocol:
DNA was extraced from ultrasonic-aspirated tissue using spin columns (DNeasy Blood & Tissue Kit, Qiagen, NL)
Library preparation was performed using the Rapid Barcoding Kit (RBK004, Oxford Nanopore Technologies, UK) according to manufacturers instructions.

value: brain tumor tissue


title: DX-BLN-074

description:
DX-BLN-074-T01A-D01A-W01
Oxford Nanopore Technologies MinION Mk 1B


title: PB02024_tumor_roi003_CancerCell

description: protein detected by antibody


title: PB02018_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: PB02018_tumor_roi003_Fibrosis

description: protein detected by antibody


title: DX-BLN-075

description:
DX-BLN-075-T01A-D01A-W01
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-071

description:
DX-BLN-071-T01A-D01A-W01
Oxford Nanopore Technologies MinION Mk 1B


title: PB02024_tumor_roi002_CancerCell

description: protein detected by antibody


title: PB02018_tumor_roi001_Fibrosis

description: protein detected by antibody


title: PB02018_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB02024_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB02018_tumor_roi001_CancerCell

description: protein detected by antibody


title: PB02024_tumor_roi002_Fibrosis

description: protein detected by antibody


title: B5M

data_processing:
To remove rat DNA,  reads were aligned to the rat genome (GCF_000001895.5)  using Bowtie2 version 2.2.5. Only unmapped  reads were retained.
Reads were aligned to Pneumocystis cariniii genome using BSMAP v2.74
further processing with methratio.py and bedtools
Assembly: GCA_001477545.1
Supplementary files format and content: bedGraph

organism: Pneumocystis carinii

growth_protocol: Infected rat lungs

extract_protocol:
Pneumocystis-infected lung tissues were cut into small pieces, homogenized in Qiagen Tissuelyser (5 times for 20 s at 1/30 frequency), then centrifuged at 15,000g for 6 min. The pellet was resuspended in Trypsin/EDTA Solution (Lonza), incubated at 37 °C for 30 min and centrifuged at 15,000g for 6 min. The pellet was washed once in PBS, resuspended in lysis buffer containing 2.9% (w/v) collagenase type I (Gibco) and 0.1% (w/v) DNase I (Sigma), incubated at 37 °C for 30 min, and centrifuged at 15,000g for 6 min. This sequential enzyme digestion was expected to remove most of the host cells and DNA as well as potentially some of Pneumocystis trophic forms. The pellet was washed three times in PBS, resuspended in 100 μl of 0.5% (w/v) Zymolyase solution (Zymo Research) and incubated at 37 °C for 1 h. Genomic DNA was extracted using the MasterPure Yeast DNA Purification Kit (Epicentre).
EZ DNA Methylation kit

value: lungs

value: infected rat 1

value: lung cell


title: PB02024_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: DX-BLN-073

description:
DX-BLN-073-T01A-D01A-W01
Oxford Nanopore Technologies MinION Mk 1B


title: PB02024_tumor_roi001_CancerCell

description: protein detected by antibody


title: DX-BLN-064

description:
DX-BLN-064
Oxford Nanopore Technologies MinION Mk 1B


title: PB02024_tumor_roi001_Fibrosis

description: protein detected by antibody


title: PB02024_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB01007_tumor_roi003_Rest_F

description: protein detected by antibody

value: stable disease (SD)


title: DX-BLN-050

description:
DX-BLN-050
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-054

description:
DX-BLN-054
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-049

description:
DX-BLN-049-T01A-D01A-W02_barcode12
Oxford Nanopore Technologies MinION Mk 1B


title: PB02024_tumor_roi003_Fibrosis

description: protein detected by antibody


title: PB01007_tumor_roi003_PanCK_T

description: protein detected by antibody


title: DX-BLN-065

description:
DX-BLN-065
Oxford Nanopore Technologies MinION Mk 1B


title: PB01007_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: DX-BLN-047

description:
DX-BLN-047
Oxford Nanopore Technologies MinION Mk 1B


title: PB01007_tumor_roi002_ImmuneCell

description: protein detected by antibody


title: DX-BLN-029

description:
DX-BLN-029
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-027

description:
DX-BLN-027
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-037

description:
DX-BLN-037
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-043

description:
DX-BLN-043
Oxford Nanopore Technologies MinION Mk 1B


title: PB01007_tumor_roi001_Rest_F

description: protein detected by antibody


title: PB01009_tumor_roi001_Fibrosis

description: protein detected by antibody

value: partial response (PR)


title: PB01009_tumor_roi002_Rest_F

description: protein detected by antibody


title: PB01009_liver_roi007_nonTumorLiver

description: protein detected by antibody


title: PB01007_tumor_roi001_PanCK_T

description: protein detected by antibody

value: PanCK


title: PB01009_tumor_roi003_ImmuneCell

description: protein detected by antibody


title: PB01007_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: DX-BLN-057

description:
DX-BLN-057
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-028

description:
DX-BLN-028
Oxford Nanopore Technologies MinION Mk 1B


title: DX-BLN-044

description:
DX-BLN-044a
Oxford Nanopore Technologies MinION Mk 1B


title: PB01009_tumor_roi003_CancerCell

description: protein detected by antibody


title: DX-BLN-042

description:
DX-BLN-042-T01A-D01A-W02
Oxford Nanopore Technologies MinION Mk 1B


title: PB01009_liver_roi007_Fibrosis

description: protein detected by antibody

value: liver


title: DX-BLN-025

description:
DX-BLN-025
Oxford Nanopore Technologies MinION Mk 1B


title: PB01009_tumor_roi001_ImmuneCell

description: protein detected by antibody


title: PB01009_tumor_roi001_CancerCell

description: protein detected by antibody


title: DX-BLN-048

description:
DX-BLN-048
Oxford Nanopore Technologies MinION Mk 1B


title: PB01009_liver_roi005_ImmuneCell

description: protein detected by antibody