title: In vivo, Top10, Cerebellum 5 weeks [T10_5wk_Cer]

first: Tyson

middle: Joel

last: Ruetz

state: CA

address: 290 Jane Stranford Way

institute: Stanford University

description: PCR ampllified DNA library

data_processing:
All of the source scripts can be found here: https://bitbucket.org/dmorgens/castle/downloads/.
fastq files were aligned to the sgRNA library sequence (“mm-Cas9-10”, or one of custom 10 gene library + control sgRNAs) to make count files using the “makeCounts” script.
The count files were then analyzed using the “analyzeCounts” CasTLE script, comparing each screen timepoint to the starting plasmid sgRNA library count file (in vitro screens) or the sequenced 24-hour SVZ count file (in vivo screens), which we sequenced in parallel with screen libraries.
P-values for all genes in each screen by running 100,000 (in vitro screens) or 10,000 (in vivo screens) permutations with the “addPermutations” CasTLE script.
For each genome-wide screen, we corrected for multiple hypotheses on the ~23,000 gene associated P-values using the Python Statsmodel module, with Benjamini/Hochberg method,
Genome_build: mm10
Supplementary_files_format_and_content: csv count files of every sgRNA

source_name: cerebellum

extract_protocol:
genomic DNAwas extracted with Qiagen QiaAmp DNA Blood Maxi Kit (51194), adding 5x107 cells per column and according to the manufacturer’s protocol.
sgRNA was amplified from the genome in 2 successive, nested PCR reactions. For the nested PCR reactions, we used either Herculase II Fusion Polymerase (Agilent, 600679) for screen 1, or Q5 DNA polymerase (Fisher Scientific, M0491L) for screens 2 and 3, and Q5 DNA polymerase for in vivo screens, according to manufacturer’s protocol. In optimizing this PCR reaction, we found that Herculase II Polymerase was outperformed by Q5 polymerase outperformed Herculase II Polymerase, Q5 polymerase requiring fewer PCR cycles to get more amplicon product, which is why we switched to Q5 DNA polymerase. We used 5 μg genomic DNA in 50 μL reactions to run on thermocycler. For the first PCR, we used primers MCB1562 (aggcttggatttctataacttcgtatagcatacattatac) and MCB1563 (acatgcatggcggtaatacggttatc) (1 µM final concentration), with PCR cycles as follows: 98°C for 2 minutes, 19 cycles of [98°C/30s, 59.1°C/30s, 72°C/45s], followed by 72°C for 3 minutes. We pooled all the PCR#1 cycle products and then used 5 µL of the pool in a second PCR reaction (PCR#2) with the same conditions but using different primers; MCB1439 (caagcagaagacggcatacgagatgcacaaaaggaaactcaccct) and a barcoded primer (aatgatacggcgaccaccgagatctacacGATCGGAAGAGCACACGTCTGAACTCCAGTCACXXXXXXCGACTCGGTGCCACTTTTTC, where XXXXXX is the 6-digit barcode for high throughput sequencing sample identification). The second PCR reaction was run for either 30 cycles (in vitro screen 1 and in vivo screens), or 18 cycles (in vitro screens 2 and 3).

tag: tissue/cell type

value: cerebellum

value: Top10 sgRNA library

tag: age-young/old

value: Old

value: Stereotaxic surgeries were performed to inject virus into the lateral ventricle of mice


title: BP1- Primary TNFR1-/- CMFs-MS1

status: Public on Nov 01 2023

type: SRA

city: Los angeles

first: Xiangming

last: Ding

state: California

address: 4650 Sunset Blvd

country: USA

institute: CHLA

library_source: transcriptomic

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Primary TNFR1-/- CMFs-MS

growth_protocol: Primary colonic myofibroblasts (CMFs) were isolated from the distal end of 16w old control (TNFR1+/-) and TNFR1-/- mice. The colon (1cm from the dentate line), cut horizontally, was stirred at 250 rpm in 5 mM EDTA/HBSS medium (without Ca++ and Mg++) at 37°C for 15 min and repeated for a total of 5 washes. Following two washes of ice-cold PBS, the tissue was digested in DMEM, low glucose, GlutaMAX™ Supplement, pyruvate plus Penicillin-Streptomycin (10,000 U/mL) with, 0.31 mg/mL Dispase and 0.25mg/mL collagenase Type XI for up to 60 minutes at 250 rpm at 37°C, until the tissue appeared stringy. Digested tissue was treated with ACK lysis buffer (4.15 g NH4Cl, 0.5 g KHCO3, 18.6 mg Na2EDTA, 400 ml H2O, pH 7.2-7.4) for 5 min and then passed through a 100‐μm cell strainer into 6-well dishes of CMF-growth medium (DMEM, low glucose, GlutaMAX™ Supplement, pyruvate plus Penicillin-Streptomycin (10,000 U/mL) with 10% FBS and 1X recombinant human insulin, human transferrin and sodium selenite (ITS) solution, and 20 ng/mL recombinant murine epidermal growth factor. After 24‐h incubation, non‐adherent cells were washed away. One week later, only myofibroblasts divided, and macrophages and epithelial cells had senesced after the first passage.

extract_protocol:
Control (TNFR1+/-) and TNFR1-/- primary CMFs (passage 6 - 8) were seeded at a density of 1x103 cells/50 µL of Matrigel into 24-well plates and were grown to 70% confluency. At D 5, CMFs were extracted from Matrigel after brief incubation at 4⁰C via centrifugation at 1200rpm for 5 min. Total RNA from primary CMFs was extracted with using the Ambion® PureLink® RNA Isolation Kit (Thermofisher Scientific, no. 12183025) according to the manufacturer’s protocol.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: RNA-Seq was performed on untreated control (TNFR1+/-) and TNFR1-/- primary CMFs.

tag: strain background

tag: tissue

value: distal colon

tag: genotype

tag: days post passage/cell type

value: d5/colonic myofibroblasts (CMFs)


title: In vivo, Top10, Cerebellum 24 hour [T10_24hr_Cer]

city: Stanford

department: Genetics

description: PCR ampllified DNA library

library_source: genomic

molecule: genomic DNA

tag: strain

tag: treatment


title: In vivo, WT mouse, Top10, OB Screen 2 [TOWTOB2]

description: PCR ampllified DNA library

source_name: Olfactory bulb

value: Olfactory bulb


title: In vivo, Cytoplasmic Ribonucleoprotein Structures, SVZ 24 hours Screen 2 [GR-S-LIB]

description: PCR ampllified DNA library

source_name: SVZ

value: SVZ


title: Increta2

type: RNA

city: Sapporo

first: Tasuku

last: Mariya

state: Hokkaido

address: South 1 West 16, Chuo-ku

country: Japan

institute: Sapporo Medical University

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H19-5191-6

hyb_protocol: Fragmented and labeled samples were hybridized to GeneChipTM Human Gene 2.0 ST Arrays (Affymetrix, Thermo Fisher Scientific).

scan_protocol: Scanning was done on a GeneChipTM Scanner 3000 7G (Affymetrix, Thermo Fisher Scientific).

data_processing: The resulting CEL files were loaded into Transcriptome Analysis Console 4.0 software package (TAC 4.0., Affymetrix) for data analysis.

label: biotin

organism: Homo sapiens

source_name: Pregnant female

label_protocol: Purified total RNA was used as input for cDNA preparation using the GeneChipTM WT Pico Reagent Kit (Affymetrix, Thermo Fisher Scientific).

growth_protocol: All placenta accreta spectums were resected with uterus at time of cecarean hysterectomy and fixed by formain. And control placenta was also fixed by formalin soon after vaginal delivery at term.

extract_protocol: RNA was isolated from macro dissected FFPE placenta with the RNeasy FFPE Kit (Qiagen), according to the manufacturer’s instructions.

value: FFPE placenta

tag: gender

value: female

tag: condition

value: Increta


title: Percreta3

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H18-6101-4

value: Percreta


title: BP6- Primary TNFR1-/- CMFs-MS6


title: Control3

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H19-7550-4

value: Control


title: Increta1

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H13-1227-3


title: Percreta1

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H15-3841-7


title: Control2

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H19-6540-4


title: Control1

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H19-6659-4


title: In vivo, Top10, OB Screen 2 [T10S-O2]

description: PCR ampllified DNA library


title: Percreta6

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H19-5961-4


title: Percreta4

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H18-6101-5


title: Percreta5

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H19-5961-3


title: In vivo, Cytoplasmic Ribonucleoprotein Structures, OB Screen 1 [GRS-O1]

description: PCR ampllified DNA library

value: Cytoplasmic Ribonucleoprotein Structures sgRNA library


title: In vivo, Top10, Cortex 5 weeks [T10_5wk_Cort]

description: PCR ampllified DNA library

source_name: cortex

value: cortex


title: In vivo, Cytoplasmic Ribonucleoprotein Structures, SVZ 24 hours Screen 1 [GRS-24]

description: PCR ampllified DNA library


title: In vivo, WT mouse, Top10, OB Screen 1 [TOWTOB1]

description: PCR ampllified DNA library


title: In vivo, Depleted, OB Screen 2 [DPS-O2]

description: PCR ampllified DNA library

value: Depleted sgRNA library


title: In vivo, Top10, SVZ 5 weeks [T10_5wk_SVZ]

description: PCR ampllified DNA library


title: In vivo, Published Regulators, OB Screen 2 [CGS-O2]

description: PCR ampllified DNA library

value: Published Regulators sgRNA library


title: In vivo, Depleted, SVZ 24 hours Screen 1/2 [DPS-24]

description: PCR ampllified DNA library


title: In vivo, Top10, Cortex 24 hour [T10_24hr_Cort]

description: PCR ampllified DNA library


title: In vivo, Top10, OB 24 hour [T10_24hr_OB]

description: PCR ampllified DNA library


title: In vivo, Top10, OB Screen 1 [T10S-O1]

description: PCR ampllified DNA library


title: In vivo, Published Regulators, SVZ 24 hours Screen2 [CGS-24]

description: PCR ampllified DNA library


title: In vivo, Top10, SVZ 24 hours, Screens 1/2 [T10S-24]

description: PCR ampllified DNA library


title: In vivo, Cytoplasmic Ribonucleoprotein Structures, OB Screen 2 [GRS-O2]

description: PCR ampllified DNA library


title: Percreta2

description:
RMA expression value derived from Expression Console software; Transcriptome Analysis Console
H15-3841-9


title: In vivo, Glucose/Human Disease, OB Screen 2 [3-CO-DIS]

description: PCR ampllified DNA library

value: Glucose/Human Disease sgRNA library


title: In vivo, Glucose/Human Disease, OB Screen 1 [DSS-O1]

description: PCR ampllified DNA library


title: TCR of Z3_E72_LN

city: Munich

first: Gildas

last: Lepennetier

address: Ismaninger Straße 22

department: Neurology

country: Germany

institute: Klinikum Rechts der Isar

description: TCR

data_processing:
Cellranger-4.0.0 with vdj_GRCm38_alts_ensembl-4.0.0 for the VDJ B and T cell analysis, default options
Cellranger-5.0.0 with mm10-2020-A for the gene expression count, default options
Genome_build: mm10
Supplementary_files_format_and_content: count
Supplementary_files_format_and_content: contig_annotations.csv

source_name: LN lumbar

growth_protocol: Thx2D2 mice develop spontaneous EAE with meningeal leukocytic infiltrates in the spinal cord. Mice were sacrificed 23±3 days after disease onset.

extract_protocol:
Blood was collected by cardiac puncture. After thorough perfusion with PBS lumbar lymph nodes, and spinal cord were dissected, and meninges were detached from the spinal cord using fine forceps. Organs were passed through cell strainers. Samples were enriched for CD45+ cells using a MACS (Miltenyi Biotech) with anti‐CD45 mouse MAb‐conjugated microbeads (Miltenyi Biotech, #130-052-301).
10x Genomics Chromium Single Cell Immune Profiling (v1)
10x Genomics single cell sequencing, without feature barcoding

treatment_protocol: mice were untreated

tag: Sex

value: male

tag: model

value: Thx2D2 EAE (experimental autoimmune encephalomyelitis)

value: Lumbar lymph node


title: In vivo, Glucose/Humand Disease, SCZ 24 hours Screen 1/2 [DSS-24]

description: PCR ampllified DNA library

value: Old

value: Stereotaxic surgeries were performed to inject virus into the lateral ventricle of mice


title: In vivo, Depleted, OB Screen 1 [DPOCOB2]

description: PCR ampllified DNA library

value: Olfactory bulb


title: In vivo, Published Regulators, OB Screen 1 [CGS-O1]

description: PCR ampllified DNA library


title: In vivo, Published Regulators, SVZ 24 hours Screen1 [CGOCSV1]

description: PCR ampllified DNA library

value: SVZ


title: BCR of Z3_E21_mELT

description: BCR

source_name: mELT from spinal cord

value: Meningeal Ectopic Lymphoid Tissue from spinal cord


title: TCR of Z3_E72_mELT

description: TCR


title: TCR of Z3_E21_mELT

description: TCR


title: TCR of Z3_E21_LN

description: TCR


title: BCR of Z3_F21_LN

description: BCR


title: BCR of Z3_F21_mELT

description: BCR


title: Old 3

city: Brooklyn

first: Ngoc

last: Luu

state: NY

address: 6 Metrotech Center

institute: New York University

hyb_protocol: he labeled cDNA is then cleaned up, fragmented, and hybridized to arrays for 16 hr at 45°C.

scan_protocol: After hybridization, the array was washed on the Fluidics Station 450/250 following the instructions. The probe array is scanned using the GeneChip® Scanner 3000 after the wash protocols are complete.

data_processing:
The data was analyzed using Affymetrix’s Transcriptome Analysis Console
Differentially expressed genes were identified based on logFC>1, Pvalue<0.05.

source_name: Old vascular smooth muscle cells

label_protocol: The resulting double-stranded cDNA is then amplified and labeled using a Biotin Allonamide Triphosphate.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen). Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation and quantified by Qubit 2.0 RNA HS assay. Reverse transcription is performed based on manufacturer’s recommendation for Affymetrix WT PLUS Kit.

treatment_protocol: No treatment

tag: age

value: 58-78 weeks

tag: cell type

value: Vascular smooth muscle cells


title: U2OS_siHELZ_DRIP_rep1

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

data_processing:
DRIP-seq reads were aligned to mouse genome sequence (hg38) by Bowtie2 version 2.4.4 with default parameter.
Aligned reads in bam file were sorted by genomic coordinate by SAMtools.
Peaks for each library were identified by MACS2 version 2.2.6 with input bam file.
DRIP-seq peaks identified from siNC and siHELZ were merged and reads were re-counted in the merged peak regions. Differential analysis was conducted by DESeq2 based on the reads count matrix in the merged peak regions and significantly changed regions were defined by FDR<0.05, log2(foldchange)>1.
The differential regions were annotated to genes by annotatePeaks.pl from HOMER version 4.11
Assembly: hg38
Supplementary files format and content: peak files

source_name: U2OS cell

extract_protocol:
Genomic DNA was extracted from ~2 million U2OS cells and fragmented with restriction enzymes (BsrGI, EcoRI, HindIII, SspI, XbaI, 30 U/each, NEB). Fragmented nucleic acids were recovered by phenol-chloroform extraction. Fragmented gDNA (5 μg) was digested with 20 U of RNase H (NEB #M0297S) for 6 hr to serve as a negative control. Fragmented gDNA or RNase H-digested DNA (5 μg) were immunoprecipitated with 8 μg of S9.6 antibody (Millipore #MABE1095) overnight at 4°C in DRIP binding buffer (10 mM sodium phosphate, 140 mM sodium chloride, 0.05% (v/v) Triton-X-100, pH 7.0). DNA-antibody complex was then incubated with 40 μL of Protein G beads (Invitrogen #10003D) for 2 hr at 4°C, and beads were washed three times with DRIP binding buffer. Antibody-captured DNA-RNA hybrids were then eluted in (50 mM Tris, 10 mM EDTA, 0.5% (v/v) SDS, pH 8.0) and subjected to phenol-chloroform extraction. The immunoprecipitated DNA-RNA hybrids were quantified by Qubit (ThermoFisher Scientific #Q32854).
DNA-RNA hybrids (10 ng) were treated with 2 U of RNase H for 1 h and then were sonicated into small fragments (~100-500 bp) using a Covaris Focused-Ultrasonicator Me220. Fragmented DNA was blunted, 5′ phosphorylated and 3’ A-tailed by NEBNext Ultra II End Prep Enzyme Mix following the manufacturer’s instruction (New England Biolabs #E7645L). An adaptor was ligated, and USER enzyme was used for U excision to yield adaptor-ligated double-strand DNA. The DNA was then PCR-amplified using barcoded PCR primers (New England Biolabs #E7335L, #E7500L). After AMPure XP bead purification (Beckman Coulter #A63881) and Qubit quantification, the libraries were sent to Admera Health for quality analysis and sequencing with Illumina with a read length configuration of 150 PE.

tag: chip antibody

value: S9.6 (Sigma, MABE1095)

tag: cell line

value: U2OS cell

value: Human Bone Osteosarcoma Epithelial Cells

value: HELZ knockdown

value: Untreated


title: U2OS_siHELZ_DRIP_rep3


title: U2OS_siHELZ_RNaseH_DRIP

value: gDNA treated with RNaseH


title: BCR of Z3_E72_mELT

description: BCR


title: BCR of Z3_E21_LN

description: BCR


title: BCR of Z3_E72_LN

description: BCR


title: iPBMC-C-5 (PCOS)

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Single-cell suspensions were prepared using Accutase (Innovative Life Technologies, San Diego, CA, USA) treated iPSC-derived ECs
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10x Genomics).

value: PBMC

value: iPSC-EC

value: PCOS


title: U2OS_siNC_DRIP_rep1

value: WT


title: U2OS_Input


title: IBMC-iPSC-01-02 (Control)

description: 10x Genomics

value: Control


title: U2OS_siNC_RNaseH_DRIP


title: Young 3

source_name: Young vascular smooth muscle cells

value: 12 weeks

value: male


title: U2OS_siNC_DRIP_rep3


title: U2OS_siHELZ_DRIP_rep2


title: U2OS_siNC_DRIP_rep2


title: iNFB-1-1 (Control)

description: 10x Genomics

source_name: skin fibroblasts

value: skin fibroblasts


title: Old 1


title: human neural precursor cells

city: Paris

first: Uwe

last: Maskos

address: 25-28 Rue du Dr Roux

department: DEPARTMENT OF NEUROSCIENCE

country: France

institute: Institut Pasteur

data_processing:
Cellranger (v.4.0.0) was used with refdata-gex-GRCh38-2020-A from Illumina as a reference with standard parameters to optain a count matrix.
Expression values were transformed using log(+1) and normalized to equal pseudo counts. Seurat’s (version 4.3.0) (Hao et al., 2021) RunPCA with 15 components and 200 variable genes, using centering and scaling was followed Seurat’s clustering function (15 PCAs, resolution = 0,5, K=10) to produce 8 clusters that were manually renamed (0-5,8 = NPC, cluster 6 = mature). Cells expressing at least one UMI of either NANOG or POU5F1 were assigned “stem-like”. All analyses and visualizations were performed using SCHNAPPs.
Assembly: refdata-gex-GRCh38-2020-A
Supplementary files format and content: tab separated, barcodes for count matrix
Supplementary files format and content: tab separated, gene names for count matrix
Supplementary files format and content: mtx format, count matrix
Supplementary files format and content: space separated, cell annotation
Supplementary files format and content: space separated, normalized filtered count matrix
Supplementary files format and content: space separated, gene annotation

source_name: brain

growth_protocol: hiPSC were induced into the neurectodermal lineage via dual smad inhibition and kept in a neuronal medium in the presence of proliferation factors to maintain the NPC state

extract_protocol:
Single Cell 3ʹ Reagent Kits v3.1 from 10X Genomics
20 000 cells were loaded onto the Chromium Next GEM Chip G of the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 from 10X Genomics.
A library was created according to the manufacturer’s protocol. The library was then sequenced with a NextSeq 500/550 High Output Kit v2.5 from Illumina.

treatment_protocol: passage 11

value: brain

value: human induced pluripotent stem cells

value: human neuronal precursor cells

value: wild type

value: dual smad inhibition


title: Young 2

value: Vascular smooth muscle cells


title: Batch1_Patient11600-15149_DH12_1

city: Oxford

first: Ahmed

middle: Ashour

last: Ahmed

state: Oxfordshire

address: John Radcliffe Hospital, Headley way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
DH12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

data_processing:
Paired-end reads from Illumina NextSeq 500 were processed and mapped using STAR
The following filters were used to eliminate cells with (1) UMI counts < 10,000 and (2) gene counts < 200
Removed genes detected in < 3 cells
Assembly: UCSC hg19
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch1
Supplementary files format and content: Gene-cell matrix table containing transcript counts for every gene in every cell for each sample in batch2

molecule: polyA RNA

source_name: Fallopian tube

growth_protocol: Fallopian tube WNT/β-catenin signaling reporter organoids were established from patient-derived cells, and expanded for 4-7 passages (each passage ~ 12 days). Endogenous WβA and non-WβA cells were isolated by FACS into RNA lysis buffer.

extract_protocol:
Isolated WβA or non-WβA cells were sorted into 96-well plates containing 4 μl lysis buffer supplemented with 0.1 μl RNase inhibitor (Clonetech), 1.9 μl 0.4% Triton X-100, 1 μl 10 μM 5‘-biotinylated oligo-dT30VN (IDT) and 1 μl 10 mM dNTP (Thermo Scientific). Cells were sorted at one cell per well, with bulk controls (10 cells) and empty well controls (0 cells) included for each plate. Plates were snap frozen on dry ice and stored at - 80 degrees C for less than 4 weeks.
Single cell cDNA synthesis and library generation were performed according to the SMART-seq2 protocol (Picelli et al., 2014), as previously described (Hu et al., 2020). Briefly, cells were lysed by removing plates from  -80 0C and heating at 72 0C for 3 min. Plates were then placed at 4 0C before adding the reverse transcription mix containing 5’-biotinylated TSO (Qiagen). PCR products were cleaned up using 0.8:1 Ampure XP beads (Beckman Coulter) with Biomek FxP Laboratory Automation Workstation (Biomek). Quality of single-cell cDNA was tested using TapeStation, as well as by single cell qPCR for GAPDH or ACTB using the QuantiNova SYBR Green PCR Kit (Qiagen). cDNA concentration was measured using Quant-iTTM PicoGreenTM dsDNA Assay Kit (Invitrogen) on the CLARIOstar Plate Reader (BMG Labtech). Wells with CT values of GAPDH or ACTB below 20 were selected as wells with good quality cDNA. Libraries from single cell cDNA were generated using miniaturized Nextera XT (Illumina) protocol (Mora-Castilla et al., 2016) with Mosquito HTS (TTP LabTech), in 384-well Endure plate (Life Technology). Library sequencing was performed by Novogene.

value: Fallopian tube


title: iPFB-1-3 (PCOS)

description: 10x Genomics


title: Batch1_Patient11600-15149_DH12_2

description:
DH12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH10_1

description:
DH10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH11_2

description:
DH11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH10_2

description:
DH10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH11_1

description:
DH11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH08_1

description:
DH08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH08_2

description:
DH08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH09_2

description:
DH09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH07_1

description:
DH07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH05_2

description:
DH05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Young 1


title: Batch1_Patient11600-15149_DH06_2

description:
DH06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH06_1

description:
DH06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Old 2

value: 58-78 weeks


title: Batch1_Patient11600-15149_DH04_2

description:
DH04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH05_1

description:
DH05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH04_1

description:
DH04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH02_2

description:
DH02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH03_1

description:
DH03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH09_1

description:
DH09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH02_1

description:
DH02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH03_2

description:
DH03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH01_2

description:
DH01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG12_1

description:
DG12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG12_2

description:
DG12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH01_1

description:
DH01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG11_2

description:
DG11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG10_2

description:
DG10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG11_1

description:
DG11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG10_1

description:
DG10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG09_1

description:
DG09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG08_2

description:
DG08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DH07_2

description:
DH07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG09_2

description:
DG09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG08_1

description:
DG08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG05_2

description:
DG05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG05_1

description:
DG05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG04_1

description:
DG04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG03_2

description:
DG03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG07_1

description:
DG07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG07_2

description:
DG07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG06_2

description:
DG06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG03_1

description:
DG03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG04_2

description:
DG04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG02_2

description:
DG02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG02_1

description:
DG02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF12_2

description:
DF12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG01_1

description:
DG01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG01_2

description:
DG01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF12_1

description:
DF12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF11_2

description:
DF11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DG06_1

description:
DG06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF08_2

description:
DF08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF07_2

description:
DF07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF07_1

description:
DF07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF05_2

description:
DF05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF10_1

description:
DF10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF10_2

description:
DF10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF09_2

description:
DF09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF09_1

description:
DF09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF04_1

description:
DF04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF03_2

description:
DF03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF06_2

description:
DF06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF06_1

description:
DF06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF05_1

description:
DF05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF04_2

description:
DF04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE12_2

description:
DE12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE12_1

description:
DE12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE10_2

description:
DE10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF03_1

description:
DF03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF02_2

description:
DF02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF08_1

description:
DF08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF01_1

description:
DF01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE11_2

description:
DE11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF02_1

description:
DF02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE11_1

description:
DE11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DF11_1

description:
DF11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE08_2

description:
DE08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE08_1

description:
DE08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE07_2

description:
DE07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE10_1

description:
DE10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE09_2

description:
DE09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE06_2

description:
DE06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group4_preOP_rep1

city: Brisbane

first: Zewen Kelvin

last: Tuong

state: QLD

address: 62 Graham Street, Centre for Children's Health Research (CCHR), South Brisbane, QLD, 4101

country: Australia

institute: The University of Queensland

data_processing:
bcl2fastq-1.8.4 software used for basecalling
Libraries were sequenced on Illumina NextSeq 500 machine with a PE 2 x 40 tag format.
Raw reads were quality checked with the FastQC tool and trimmed using the Trimmomatic tool.
RNAseq reads were aligned to the rn6 reference transcriptome and quantified using salmon
Genome_build: rn9
Supplementary_files_format_and_content: text file containing raw quants

organism: Rattus norvegicus

source_name: Femur

extract_protocol:
Femurs and fracture hematomas were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: male SAS Fischer

value: Femur

tag: weight

tag: healing model

value: preOP


title: Batch1_Patient11600-15149_DE09_1

description:
DE09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group4_preOP_rep2


title: Batch1_Patient11600-15149_DE06_1

description:
DE06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group3_nonunion_rep3

source_name: Fracture hematoma

value: Fracture hematoma from femoral defect

value: 5.0 mm defect

value: nonunion


title: Batch1_Patient11600-15149_DF01_2

description:
DF01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE04_2

description:
DE04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group2_delayed_healing_rep2

value: 1.5 mm defect


title: Batch1_Patient11600-15149_DE02_2

description:
DE02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD12_2

description:
DD12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD12_1

description:
DD12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: WT_1_Pol-II

city: Bar Harbor

first: Joel

middle: H

last: Graber

state: ME

address: 159 Old Bar Harbor Rd

department: Bioinformatics Core

institute: MDI Biological Laboratory

data_processing:
trimmomatic 0.38, arguments -Xms1000m -Xmx1000m, all other arguments default
bwa version 0.7.17-r1188, with default parameters, aligned to sacCer3 (ensembl release-93), indexed by bwa with default parameters.
DeepTools version 3.1.2, command bamCoverage with parameters --smoothLength 21 --effectiveGenomeSize 12400000 --normalizeUsing RPGC -bs 1 -of bigwig -p 8 --minMappingQuality 1
Replicate samples were combined with DeepTools version 3.1.2, command bigwigCompare with options --operation add --bs 10 -p 4
Chip enrichment was calculated with DeepTools version 3.1.2, command bigwigCompare with options --operation ratio --bs 10 -p 4
Gene body count matrixes for pol2 and input seq were generated with DeepTools version 3.1.2, using command computeMatrix scaled-regions, using a gene-definition bed file generated from the feature table downloaded from the Yeast Genome Database in October 2019.
Genome_build: sacCer3 (Ensembl release 93)
Supplementary_files_format_and_content: files pcf11_chip_input.counts and pcf11_chip_pol2.counts.txt are tab-separated value text table files that list the sequence counts assigned ot each gene as described in the methods
Supplementary_files_format_and_content: files *.bw are bigwig-formatted coverage files of the chip-seq data, either for the targetd RNA Polymerase II associated samples or for the matched input data

organism: Saccharomyces cerevisiae

source_name: cell

growth_protocol: Yeast cells (400 ml) were grown to OD600 of 0.5, fixed with 1.035% formaldehyde for 15 minutes and neutralized with 0.135 M glycine for 5 minutes.

extract_protocol:
Samples were de-crosslinked overnight at 65°C and then treated with Proteinase K for 2-4 hours at 42°C. LiCl (to 0.4 M), 20 mg glycogen and 1 ml 100% ethanol were added to precipitate the DNA. The DNA pellets were washed in 70% ethanol and were further purified using MinElute columns (Qiagen). An aliquot of sample was not immunoprecipitated, but deproteinized and used as input
The eluted DNA from two biological replicates of each strain was submitted to the Tufts Genomics Core Facility for TruSeq ChIP library preparation and for 50 nt single-end sequencing on the Illumina HiSeq 2500 system.

treatment_protocol: Washed cells were lysed in FA-lysis buffer (50 mM HEPES-KOH, pH 7.9; 150 mM NaCl; 1% Triton X-100; 1 mM EDTA; 0.1% sodium deoxycholate; 0.1% SDS) with grinding in liquid nitrogen. Crosslinked chromatin was sheared in a final volume of 4 ml FA-lysis buffer using a Branson water bath sonicator at 4°C for 8 minutes. The resulting 4 ml of chromatin was incubated with 40 ml of the anti-pan CTD mouse monoclonal antibody, 4H8 (Santa Cruz) and 200 ml pre-washed protein G beads for 5 hours at 4°C. The beads were washed once with each of the following buffers: FA-lysis buffer + 275 mM NaCl; FA-lysis buffer + 500 mM NaCl; LiCl buffer (10 mM Tris-Cl, 1 mM EDTA, 0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, pH 8.0); and 10 mM Tris-Cl, 1 mM EDTA (TE). Chromatin was then eluted in two steps: 1) in 150 ml TE + 1% SDS at 65°C for 15 minutes, and 2) in 150 ml TE + 0.67% SDS at 65°C for 10 minutes.

value: cell

value: w303 strain;MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,112; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2-V5-PCF11-MYC]

value: anti-pan CTD mouse monoclonal antibody

value: glucose

tag: molecule subtype

value: DNA-bound protein


title: WT_2_Pol-II


title: WT_2_input

value: none (input)

value: DNA


title: Batch1_Patient11600-15149_DD11_1

description:
DD11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group4_preOP_rep3


title: Pcf11-13_2_input

value: w303 strain;MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,112; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2-pcf11-13]


title: Batch1_Patient11600-15149_DD10_1

description:
DD10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Batch1_Patient11600-15149_DE07_1

description:
DE07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD09_2

description:
DD09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Pcf11-DNL_2_Pol-II

value: w303 strain; MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,12; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2--V5-pcf11-deltaN-linkMYC]


title: Batch1_Patient11600-15149_DD09_1

description:
DD09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD08_2

description:
DD08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: mouse kidney, UUO7D, 5AZA, sample 2

city: AUGUSTA

first: Qingqing

last: Wei

state: Georgia

address: 1460 Laney Walker Blvd.

department: Cellular Biology & Anatomy

institute: Augusta University

data_processing:
To map the sequencing reads from RRBS, the mouse genome (mm9) was indexed by converting all C’s and G’s to T’s and A’s, respectively, which results in two different reference databases representing both strands. The cleaned reads was used to map to each of the two reference databases using Bowtie (Langmead et al., 2009) after converting all C’s to T’s. For each read, an in-house script computed the best of all alignments for the different loci using two different reference databases based on the number of mismatches after realigning the original read and reference sequences. Another in-house script determined the methylation status of each cytosine residue by comparing the bisulfite-converted sequence to the reference sequence. The third script piled reads for each cytosine in the reference genome and counted the numbers of reads that contained methylated and unmethylated cytosines, respectively. Finally the methylation of each CpG site was defined as the fraction of methylated reads to that of methylated and unmethylated reads combined. CpGs with < 5 reads were filtered out for further analyses. We used windows of length 200bp with an overlap of 100bp between to identify differentially methylated regions (DMRs) by summing the numbers of methylated and unmethylated CpGs in reads, respectively.
Methylation calculation: The methylation level [(# of methylated)/(# of methylated + # of unmethylated)] was calculated after measuring the amount of methylation (CG->CG) and unmethylation (CG->TG) in the CpG position. Only CpGs that are covered by at least 10 sequencing reads were included.
Assembly: mm9
Supplementary files format and content: bed

source_name: Kidney

extract_protocol:
The genomic DNA samples were extracted from mouse kidney cortex and outer medulla with QIAmp DNA Blood Mini kit from Qiagen (Germantown, MD) according to the manufacturer’s manual.
RRBS was performed according to a previously published protocol (Gu et al. 2010; Meissner et al. 2008) with minor modifications. For each sample, 1  g genomic DNA was first digested overnight using 20 units of MspI (New England Biolabs, NEB). The digested DNA was end-repaired and adenylated in a 20  l reaction consisting of 10U of Klenow fragments (exo-, Enzymatics, MA, USA), and 2  l premixed nucleotide triphosphates (1 mM dGTP, 10 mM dATP, 1 mM methylated dCTP). The reaction was incubated at 30 C for 30 min followed by 37 C for an additional 30 min. The methylated Illumina adapters were ligated with adenylated DNA fragments in a 20  l reaction containing 1  l concentrated T4 ligase (Enzymatics) at room temperature for 15 minutes. The ligation products were gel-selected for fragments with insertion sizes of 40 to 120 bp and 120 to 220 base pairs as previously suggested (Gu et al. 2010; Meissner et al. 2008).  Bisulfite treatment of the sequencing library was conducted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) according to manufacturer's protocol. The final libraries were generated by PCR amplification of 5 ?m of bisulfite-converted template using PfuTurbo Cx Hotstart polymerase and Illumina pair-end PCR primers (PE1.0 and PE2.0).

treatment_protocol: For UUO surgery, mice were anesthetized and the left ureter was ligated twice with suture and a cut was made between the two ligations. For bilateral kidney ischemia surgery, mice were anesthetized and both renal pedicles were clamped for 25 minutes. And then the clips were released for reperfusion. The sham-operated mice experienced similar surgery operations but without ureter ligation and cut or renal pedicle clamping. For 5AZA treatment, 1mg/kg/day 5AZA in saline was administered through I.P. injection.

value: Kidney

value: male

value: wild type


title: group3_nonunion_rep2

value: male SAS Fischer

value: Fracture hematoma from femoral defect


title: Batch1_Patient11600-15149_DE05_2

description:
DE05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE05_1

description:
DE05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group2_delayed_healing_rep3


title: Batch1_Patient11600-15149_DE03_2

description:
DE03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE03_1

description:
DE03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group2_delayed_healing_rep1


title: Batch1_Patient11600-15149_DE04_1

description:
DE04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group1_normal_healing_rep3

value: 0.5 mm defect


title: group3_nonunion_rep1

value: 5.0 mm defect

value: nonunion


title: group1_normal_healing_rep2


title: Batch1_Patient11600-15149_DE02_1

description:
DE02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE01_2

description:
DE01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DE01_1

description:
DE01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: group1_normal_healing_rep1


title: WT_1_input

value: cell

value: w303 strain;MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,112; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2-V5-PCF11-MYC]


title: mouse kidney, UUO7D, 5AZA, sample 1


title: Pcf11-13_1_Pol-II

value: anti-pan CTD mouse monoclonal antibody

value: glucose


title: Batch1_Patient11600-15149_DD11_2

description:
DD11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Pcf11-13_1_input

value: none (input)


title: Pcf11-13_2_Pol-II

value: DNA-bound protein


title: Pcf11-DNL_2_input

value: DNA


title: Batch1_Patient11600-15149_DD10_2

description:
DD10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Pcf11-DNL_1_Pol-II

value: w303 strain; MAT alpha; ura3-1; trp1-delta; ade2-1; leu2-3,12; his3-11,15; pcf11-delta::TRP1/[pRS325-LEU2--V5-pcf11-deltaN-linkMYC]


title: Batch1_Patient11600-15149_DD05_2

description:
DD05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD08_1

description:
DD08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD07_2

description:
DD07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Foxc2_podocyte_mTmG_PBS_rep3

city: Boston

first: Jordan

last: Kreidberg

state: MA

address: 99 Brookline Ave

institute: BIDMC Research North

data_processing:
Data was processed following the Nextflow nf-core/chipseq (https://nf-co.re/chipseq) pipeline and filters with default parameters.
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak

source_name: podocytes

extract_protocol:
Samples were fixed with 1% formaldehyde in PBS for 5 min at room temperature before termination with 0.125 M glycine. Cells were lysed in sonication buffer and cross-linked chromatin was sonicated to obtain DNA fragments of 200-600 bp.
ChIP-seq libraries were prepared using NEBNext DNA library preparation reagents (E6040) and the protocol and reagent concentrations described in the Illumina Multiplex ChIP-seq DNA sample Prep Kit. Libraries were indexed using a single indexed PCR primer. Libraries were quantified by Qubit (Invitrogen) and sequenced using a HiSeq 2000 (Illumina) to generate 50-bp single-end reads.

value: podocytes

value: Abcam b5060


title: mouse kidney, UUO7D, sample 1

value: Kidney

value: male

value: wild type

value: unilateral ureter obstruction


title: Batch1_Patient11600-15149_DD03_2

description:
DD03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD02_2

description:
DD02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Foxc2_podocyte_mTmG_PBS_rep1


title: Batch1_Patient11600-15149_DD02_1

description:
DD02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD01_2

description:
DD01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD06_2

description:
DD06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD07_1

description:
DD07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Pcf11-DNL_1_input


title: mouse kidney, bilateral kidney ischemia 25 minutes and 1 week reperfusion

value: bilateral kidney ischemia 1 week reperfusion


title: Batch1_Patient11600-15149_DD06_1

description:
DD06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD01_1

description:
DD01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: mouse kidney, sham sample 1 for UUO7D

value: sham


title: Batch1_Patient11600-15149_DD05_1

description:
DD05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC12_2

description:
DC12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: mouse kidney, UUO7D, sample 2


title: Batch1_Patient11600-15149_DC12_1

description:
DC12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Foxc2_podocyte_mTmG_PBS_rep2


title: Batch1_Patient11600-15149_DD04_1

description:
DD04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD03_1

description:
DD03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Foxc2_podocyte_mTmG_ADR_rep3


title: Batch1_Patient11600-15149_DC11_1

description:
DC11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC11_2

description:
DC11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: mouse kidney, sham for kidney ischemia/reperfusion


title: mouse kidney, bilateral kidney ischemia 25 minutes and 1 month reperfusion

value: bilateral kidney ischemia 1 month reperfusion


title: Foxc2_podocyte_mTmG_ADR_rep1


title: Batch1_Patient11600-15149_DC10_1

description:
DC10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DD04_2

description:
DD04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Yolk sac Rsu1-KO rep3

city: Shenzhen

first: Yi

last: Deng

state: Guangdong Province

address: 1088 Xueyuan Blvd., Nanshan District

department: Department of Biology

country: China

institute: Southern University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38 (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: Yolk sac

extract_protocol:
Yolk sacs were removed, flash frozen on dry ice,ground in Trizol with TissueLyser (SAIERTE) to extract total RNA with RNA extraction kit (Transgen, ER501-01). The quality of the total RNA was assessed using Agilent2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: yolk sac


title: Yolk sac Rsu1-KO rep2


title: Yolk sac Rsu1-KO rep1


title: Batch1_Patient11600-15149_DC10_2

description:
DC10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Yolk sac WT rep3


title: Yolk sac WT rep1


title: Batch1_Patient11600-15149_DC09_1

description:
DC09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Foxc2_podocyte_mTmG_ADR_rep2


title: Batch1_Patient11600-15149_DC06_2

description:
DC06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC08_1

description:
DC08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC07_2

description:
DC07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC05_2

description:
DC05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC09_2

description:
DC09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC05_1

description:
DC05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC08_2

description:
DC08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC07_1

description:
DC07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC04_2

description:
DC04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Yolk sac WT rep2


title: Batch1_Patient11600-15149_DC03_2

description:
DC03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Cancer non stem cells from moderately differentiated colorectal cancer tissue (Group Cancer Non Stem Cell),  biol rep 2

city: New Delhi

first: Aditi

last: Bhattacharya

state: Delhi

address: Lab No. 3027A, Department of Biochemistry, Teaching Block, AIIMS

department: Biochemistry

country: India

institute: All India Institute of Medical Science, New Delhi

description: [[desc]]

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Cancer non stem cells from moderately differenentiated colorectal cancer tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the One-Color Low total RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification. Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using Trizol reagent. The protocol includes brief pipetting and vorteing, followed by phase seperation by chloroform and precipitation using iso-propanol. This was followed by washing by 75% ethanol and elution in nuclease-free waster. Total RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: Tissue was treated with collagenase IV to get a homogenous suspension. Cells were stained with antibodies (CD44, CD166 for cancer stem cells and CD29, Lgr5 for normal stem cells) on the basis of which dual marker positive cells were isolated.

value: Colorectal cancer tissue

value: Cancer non stem cells

value: Male


title: Normal Non-stem cells from normal colon (Group Normal Cells),  biol rep 3

description: [[desc]]

source_name: Non stem cells from normal colon

value: Colorectal normal tissue

value: Non stem cells

value: Female


title: Cancer non stem cells from moderately differentiated colorectal cancer tissue (Group Cancer Non Stem Cell),  biol rep 1

description: [[desc]]


title: Cancer stem cells from moderately differentiated colorectal cancer tissue (Group Cancer Stem Cell),  biol rep 2

description: [[desc]]

source_name: Cancer stem cells from moderately differenentiated colorectal cancer tissue

value: Cancer stem cells


title: Anti-PD-1-plus-anti-CTLA-4-A

city: Houston

first: Arjun

state: TX

address: 1155 Pressler Street

department: Epidemiology

institute: University of Texas MD Anderson Cancer Center

data_processing:
Sequence reads were quality controlled using FastQC and trimmed for adapters using trimmomatic v0.39
Trimmed sequence reads were pseudomapped and quantified to the GencodeM27 mouse transcriptomic gene set using Salmon v1.5.0
Transcript counts were imported and summarized to gene counts using tximeta v1.16.1
Genes with less than 5 counts for 18 or more samples were removed. Counts/TPM were normalized using DESeq2's variance-stabilized transformation
Assembly: GRCm39
Supplementary files format and content: tab delimited file with raw counts for each sample
Supplementary files format and content: tab delimited file with length-scaled TPM for each sample

source_name: SCCVII

extract_protocol:
mini RNA isolation kit from Qiagen (Cat # 74014), CA)
KAPA mRNA hyperprep method as per public protocol

value: SCCVII

value: head and neck cancer cells


title: Normal Non-stem cells from normal colon (Group Normal Cells),  biol rep 2

description: [[desc]]


title: APG-plus-Anti-PD-1-plus-anti-CTLA-4-A

description: APG-plus-Anti-PD-1-plus-anti-CTLA-4-A_S7


title: Anti-CD8antibody-A


title: Batch1_Patient11600-15149_DC02_2

description:
DC02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

value: Fallopian tube


title: Cancer stem cells from moderately differentiated colorectal cancer tissue (Group Cancer Stem Cell),  biol rep 3

description: [[desc]]


title: Batch1_Patient11600-15149_DC04_1

description:
DC04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: APG-157-plus-anti-PD-1-A


title: Batch1_Patient11600-15149_DC03_1

description:
DC03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Anti-CTLA-4-A


title: Batch1_Patient11600-15149_DC06_1

description:
DC06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC01_2

description:
DC01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Cancer stem cells from moderately differentiated colorectal cancer tissue (Group Cancer Stem Cell),  biol rep 1

description: [[desc]]


title: Normal stem cells from normal colon (Group Normal Stem Cell),  biol rep 2

description: [[desc]]

source_name: Normal stem cells from normal colon

value: Normal stem cells


title: Batch1_Patient11600-15149_DC01_1

description:
DC01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Normal stem cells from normal colon (Group Normal Stem Cell),  biol rep 3

description: [[desc]]


title: Normal Non-stem cells from normal colon (Group Normal Cells),  biol rep 1

description: [[desc]]


title: Normal stem cells from normal colon (Group Normal Stem Cell),  biol rep 1

description: [[desc]]


title: Cancer non stem cells from moderately differentiated colorectal cancer tissue (Group Cancer Non Stem Cell),  biol rep 3

description: [[desc]]


title: Anti-PD-1-A


title: APG-157-plus-anti-CTLA-4-A


title: Anti-CD8-plus-APG-plus-anti-CTLA-4-B

description: Anti-CD8-plus-APG-plus-anti-CTLA-4-B_S20


title: Batch1_Patient11600-15149_DB12_1

description:
DB12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB12_2

description:
DB12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DC02_1

description:
DC02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB11_2

description:
DB11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB10_2

description:
DB10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB11_1

description:
DB11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Anti-PD-1-plus-anti-CTLA-4-B


title: APG-plus-Anti-PD-1-plus-anti-CTLA-4-B

description: APG-plus-Anti-PD-1-plus-anti-CTLA-4-B_S17


title: Batch1_Patient11600-15149_DB09_1

description:
DB09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: APG-157-plus-anti-CTLA-4-B


title: Anti-CD8antibody-B


title: APG-157-plus-anti-PD-1-B


title: APG-157-B


title: Batch1_Patient11600-15149_DB08_1

description:
DB08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB09_2

description:
DB09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Anti-PD-1-B


title: Anti-CTLA-4-B


title: Batch1_Patient11600-15149_DB07_2

description:
DB07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB06_2

description:
DB06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB07_1

description:
DB07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Anti-CD8-plus-APG-plus-anti-CTLA-4-A

description: Anti-CD8-plus-APG-plus-anti-CTLA-4-A_S10


title: control-B

value: control


title: Batch1_Patient11600-15149_DB06_1

description:
DB06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: control-A


title: Batch1_Patient11600-15149_DB05_2

description:
DB05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: APG-157-A


title: 4XKO, day4, rep3

city: Aarhus

first: Mark

last: Denham

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

description:
4X_H9_counts_TPM.txt
4XKO_D4_3

data_processing:
The reads were aligned to the Human genome build hg38 (Ensemble release 92) using HISAT2 aligner (v2.1.0). Transcript quantification was performed using FeatureCount (v1.6.4), and the read counts were normalized for effective gene length and sequencing depth to yield transcripts per kilobase million (TPM).
Assembly: hg38
Supplementary files format and content: count table
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: hESCs

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit and treated with DNase I according to a standard protocol
Total RNA was subjected to oligo dT-based mRNA enrichment. Sequencing of 100 bp paired-end reads was performed on the DNBseq platform. More than 20 million clean reads were obtained per sample.

value: CNP

value: GBX2 CDX1 CDX2 CDX4 knockout

tag: time


title: 4XKO, day4, rep2

description:
4X_H9_counts_TPM.txt
4XKO_D4_2


title: Batch1_Patient11600-15149_DB08_2

description:
DB08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv

tag: tissue


title: Batch1_Patient11600-15149_DB05_1

description:
DB05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4XKO, day4, rep1

description:
4X_H9_counts_TPM.txt
4XKO_D4_1

tag: genotype


title: Batch1_Patient11600-15149_DB04_2

description:
DB04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB04_1

description:
DB04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4XKO, hESCs, rep3

description:
4X_H9_counts_TPM.txt
4XKO_ES_3

value: hESCs


title: Batch1_Patient11600-15149_DB10_1

description:
DB10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4XKO, hESCs, rep1

description:
4X_H9_counts_TPM.txt
4XKO_ES_1


title: Batch1_Patient11600-15149_DB03_2

description:
DB03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GBX2KO, day4, rep3

description:
4X_H9_counts_TPM.txt
GBX2KO_D4_3

value: GBX2 knockout


title: Batch1_Patient11600-15149_DB02_2

description:
DB02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB03_1

description:
DB03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4XKO, hESCs, rep2

description:
4X_H9_counts_TPM.txt
4XKO_ES_2


title: GBX2KO, day4, rep1

description:
4X_H9_counts_TPM.txt
GBX2KO_D4_1


title: Batch1_Patient11600-15149_DA12_2

description:
DA12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GBX2KO, hESCs, rep2

description:
4X_H9_counts_TPM.txt
GBX2KO_ES_2


title: Batch1_Patient11600-15149_DB01_1

description:
DB01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GBX2KO, hESCs, rep1

description:
4X_H9_counts_TPM.txt
GBX2KO_ES_1


title: GBX2KO, hESCs, rep3

description:
4X_H9_counts_TPM.txt
GBX2KO_ES_3


title: GBX2KO, day4, rep2

description:
4X_H9_counts_TPM.txt
GBX2KO_D4_2


title: Batch1_Patient11600-15149_DA11_2

description:
DA11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA11_1

description:
DA11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB01_2

description:
DB01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DB02_1

description:
DB02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, day4, rep2

description:
4X_H9_counts_TPM.txt
H9_D4_2

value: WT


title: H9, day4, rep3

description:
4X_H9_counts_TPM.txt
H9_D4_3


title: Batch1_Patient11600-15149_DA10_2

description:
DA10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, day4, rep1

description:
4X_H9_counts_TPM.txt
H9_D4_1


title: Batch1_Patient11600-15149_DA12_1

description:
DA12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA10_1

description:
DA10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, hESCs, rep2

description:
4X_H9_counts_TPM.txt
H9_ES_2


title: Batch1_Patient11600-15149_DA09_2

description:
DA09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, hESCs, rep3

description:
4X_H9_counts_TPM.txt
H9_ES_3


title: Batch1_Patient11600-15149_DA09_1

description:
DA09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, hESCs, rep1

description:
4X_H9_counts_TPM.txt
H9_ES_1


title: Batch1_Patient11600-15149_DA08_1

description:
DA08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA07_2

description:
DA07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA07_1

description:
DA07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA06_2

description:
DA06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA06_1

description:
DA06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 3, BBzeta CAR, un-stimulated

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: According to manufacturer's protocol (Nanostring); used commercially available kit catalog number XT-CSO-MIM1-12 were performed using NanoString XT CAR-T Panel Standard.

data_processing: Data were processed with nSolver 4.0 software using Default settings.

source_name: Primary human T cells

growth_protocol: Buffy coats from healthy donors  were used to isolate Peripheral Blood Mononuclear Cells (PBMCs) by density Centrifugation (Pancoll). The cells were activated with anti-CD3 and anti-CD28 antibodies (1µg/ml) and 500U/ml of human IL-2 for 48-72 hr. T cell purity and activation were verified by Flow Cytometry with anti-CD3 and anti-CD69 antibodies. Primary human T cells were lentivirally transduced with 5 g/mL Proteamine Sulfate (PS) in the presence of 500U/ml of human IL-2 using a Multiplicity of Infection (MOI) equal to 4, unless otherwise indicated by spin infection (1800 rpm, 30°C, 90 min). CAR T cells were maintained with RPMI-1640 medium plus 5% fetal calf serum, HEPES, Pen-strep and -mercaptoethanol and 100U/ml of human IL-2.

extract_protocol: RNA was isolated using the QIAGEN Rneasy following manufacturer instructions.

treatment_protocol: After 6 days of transduction, 5-6 x 106 CAR T cells were stimulated 24 h with Nalm6 1:1 ratio wile 5-6 x 106 CAR T cells were maintained without stimulation.

value: Primary human T cells

tag: stimulated with target cells (24h)

value: NO


title: Healthy donor 3, BBdelta CAR, un-stimulated

scan_protocol: According to manufacturer's protocol (Nanostring); used commercially available kit catalog number XT-CSO-MIM1-12 were performed using NanoString XT CAR-T Panel Standard.


title: Batch1_Patient11600-15149_DA05_2

description:
DA05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Panel standard_3

source_name: Panel standard

label_protocol: According to manufacturer's protocol (Nanostring); used commercially available kit catalog number XT-CSO-MIM1-12


title: Batch1_Patient11600-15149_DA04_2

description:
DA04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA04_1

description:
DA04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA05_1

description:
DA05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 3, Mock, un-stimulated


title: Healthy donor 3, BBzeta CAR, stimulated with target cells

value: yes


title: Batch1_Patient11600-15149_DA03_2

description:
DA03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 3, BBgamma CAR, stimulated with target cells


title: Batch1_Patient11600-15149_DA02_2

description:
DA02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 3, BBepsilon CAR, stimulated with target cells


title: Healthy donor 3, BB CAR, un-stimulated


title: Batch1_Patient11600-15149_DA02_1

description:
DA02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA01_2

description:
DA01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA03_1

description:
DA03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA08_2

description:
DA08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 3, BB CAR, stimulated with target cells


title: Healthy donor 3, Mock, stimulated with target cells


title: Panel standard_2


title: Healthy donor 2, BBzeta CAR, un-stimulated


title: Batch1_Patient11600-15149_CH12_1

description:
CH12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH12_2

description:
CH12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_DA01_1

description:
DA01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 3, BBdelta CAR, stimulated with target cells


title: Healthy donor 2, BBdelta CAR, un-stimulated


title: Healthy donor 3, BBepsilon CAR, un-stimulated


title: Healthy donor 2, BBepsilon CAR, un-stimulated


title: Batch1_Patient11600-15149_CH11_1

description:
CH11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH10_2

description:
CH10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 2, BB CAR, un-stimulated


title: Healthy donor 2, Mock, un-stimulated


title: Batch1_Patient11600-15149_CH11_2

description:
CH11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 2, BBgamma CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH09_2

description:
CH09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 2, BBdelta CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH10_1

description:
CH10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 2, BBzeta CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH08_1

description:
CH08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH09_1

description:
CH09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH07_2

description:
CH07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH08_2

description:
CH08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 2, Mock, stimulated with target cells


title: Healthy donor 2, BBepsilon CAR, stimulated with target cells


title: Healthy donor 2, BB CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH07_1

description:
CH07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH06_2

description:
CH06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Panel standard_1


title: Healthy donor 1, BBdelta CAR, un-stimulated


title: Batch1_Patient11600-15149_CH06_1

description:
CH06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH05_1

description:
CH05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CH05_2

description:
CH05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BBepsilon CAR, un-stimulated


title: Batch1_Patient11600-15149_CH04_1

description:
CH04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BB CAR, un-stimulated


title: Healthy donor 1, Mock, un-stimulated


title: Batch1_Patient11600-15149_CH04_2

description:
CH04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BBdelta CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH03_2

description:
CH03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BBgamma CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH02_2

description:
CH02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BBepsilon CAR, stimulated with target cells


title: KRV36, light-adapted cells, 24 hours after the shift to dark, rep3

city: Trebon

first: Karel

middle: Vaclav

last: Kopejtka

address: Novohradska

department: Centre Algatech

country: Czech Republic

institute: Institute of Microbiology Czech Acad. Sci.

data_processing:
Raw reads were processed, and differential gene expression was assessed as described before (Kopejtka et al., 2020).
Quality filtered reads were mapped to the S. rosea KRV36 genome (GenBank accession number NZ_CP085081.1) using bowtie2.
FeatureCounts was used to assess the number of reads per gene.
Normalization and identification of significantly differentially regulated genes (FDR < 0.05) was performed with edgeR.
Assembly: NZ_CP085081.1
Supplementary files format and content: text file includes counts for each sample

organism: Sediminicoccus rosea

source_name: S. rosea KRV36

growth_protocol: S. rosea KRV36 was grown at 23 °C in half-strength R2A medium supplemented with 160 mg of MgCl2, 60 mg of CaCl2, 10 mL of SL-4 micronutrients (cf. DSMZ medium 462) and 2 mL of vitamins (cf. DSMZ medium 462) per litre of full medium. Batch cultures continuously illuminated by LED panels providing 100 μmol photon m-2 s-1 of white light were aerated by bubbling and stirring (<100 rpm).

extract_protocol:
Cells from triplicate cultures were harvested by centrifugation, resuspended in 1 mL PGTX extraction solution (Pinto et al., 2009) and immediately frozen in liquid nitrogen. RNA was extracted as described earlier (Kopejtka et al., 2020).
Libraries were generated according to the protocol of Shishkin et al. (2015) including rRNA removal with the RiboZero Kit (Illumina, USA) and sequenced on a NovaSeq 6000 (Illumina, USA) in paired-end mode with 100 cycles in total.

treatment_protocol: Erlenmeyer flasks containing 100 mL of medium were inoculated with 2.5 mL of pre-culture and placed on an orbital shaker (150 rpm). Two flasks were incubated in the dark, two were exposed to light intensities of 100 μmol photon m-2 s-1 for 72 hours. Then, samples were collected from all four flasks, the cultures’ light regime was reversed, and the sampling followed the cultures after 2, 4, 8, and 24 hours into their dark-light and light-dark transitions, respectively.

tag: strain

value: S. rosea KRV36


title: Batch1_Patient11600-15149_CH03_1

description:
CH03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, Mock, stimulated with target cells


title: Healthy donor 1, BB CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CH02_1

description:
CH02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, 24 hours after the shift to dark, rep2

tag: treatment


title: KRV36, light-adapted cells, 24 hours after the shift to dark, rep1


title: Batch1_Patient11600-15149_CH01_2

description:
CH01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, 8 hours after the shift to dark, rep3


title: Batch1_Patient11600-15149_CG12_2

description:
CG12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BBgamma CAR, un-stimulated


title: KRV36, light-adapted cells, 8 hours after the shift to dark, rep2


title: Batch1_Patient11600-15149_CG12_1

description:
CG12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Healthy donor 1, BBzeta CAR, stimulated with target cells


title: Batch1_Patient11600-15149_CG11_1

description:
CG11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG11_2

description:
CG11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, 8 hours after the shift to dark, rep1


title: KRV36, light-adapted cells, 4 hours after the shift to dark, rep2


title: Batch1_Patient11600-15149_CG10_2

description:
CG10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, 4 hours after the shift to dark, rep3


title: KRV36, light-adapted cells, 4 hours after the shift to dark, rep1


title: Batch1_Patient11600-15149_CG10_1

description:
CG10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, 2 hours after the shift to dark, rep2


title: Batch1_Patient11600-15149_CG09_2

description:
CG09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG07_2

description:
CG07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG08_1

description:
CG08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG08_2

description:
CG08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, 2 hours after the shift to dark, rep1


title: Batch1_Patient11600-15149_CH01_1

description:
CH01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, rep2

value: cells adapted to continuous light for 72 hours


title: KRV36, light-adapted cells, rep1


title: Batch1_Patient11600-15149_CG09_1

description:
CG09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, dark-adapted cells, 24 hours after the shift to light, rep2


title: Batch1_Patient11600-15149_CG07_1

description:
CG07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG06_1

description:
CG06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, light-adapted cells, rep3


title: KRV36, dark-adapted cells, 24 hours after the shift to light, rep1


title: Batch1_Patient11600-15149_CG06_2

description:
CG06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, dark-adapted cells, 8 hours after the shift to light, rep2


title: Batch1_Patient11600-15149_CG05_1

description:
CG05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG05_2

description:
CG05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, dark-adapted cells, 8 hours after the shift to light, rep1


title: KRV36, dark-adapted cells, 4 hours after the shift to light, rep2


title: KRV36, dark-adapted cells, 4 hours after the shift to light, rep1


title: KRV36, light-adapted cells, 2 hours after the shift to dark, rep3


title: KRV36, dark-adapted cells, 2 hours after the shift to light, rep2


title: Batch1_Patient11600-15149_CG04_1

description:
CG04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, dark-adapted cells, 2 hours after the shift to light, rep1


title: Batch1_Patient11600-15149_CG04_2

description:
CG04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG02_2

description:
CG02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG03_2

description:
CG03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: KRV36, dark-adapted cells, rep1

value: cells adapted to continuous dark for 72 hours


title: KRV36, dark-adapted cells, rep2


title: Batch1_Patient11600-15149_CG02_1

description:
CG02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG01_2

description:
CG01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF12_2

description:
CF12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG01_1

description:
CG01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF11_1

description:
CF11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF10_1

description:
CF10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF10_2

description:
CF10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF09_2

description:
CF09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CG03_1

description:
CG03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF08_2

description:
CF08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF09_1

description:
CF09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: E-V12, mechanical ventilation_12hr with electrical stimulation_rep3

city: Nishinomiya

first: Yutaka

last: Hirata

state: Hyogo

address: 1-1 Mukogawa-cho

department: Integrative Physiology

institute: Hyogo Medical University

description: Gene expression data from diaphragm

hyb_protocol: GeneChip™ arrays (Rat ClariomTM S) were hybridized with biotin-labeled cDNA samples at 45°C for 16 hours (60 rpm) using a GeneChip™ Hybridization Oven 645.

scan_protocol: The arrays were washed and stained with a GeneChip™ Fluidics Station 450 and scanned on an Affymetrix Gene Chip Scanner 3000 7G using Command Console Software.

data_processing: The signal values of the GeneChip™ array were normalized based on the total intensity of the array using the SST-RMA algorithm implemented in Transcriptome Analysis Console (TAC) v4.0 software (Thermo Fisher Scientific, MA, USA).

source_name: Rats with tracheostomy and abdominal incision, electrical stimulation applied during 12 hours of mechanical ventilation

label_protocol: From 250 ng of total RNA in each group, fragmented and biotin-labeled complementary deoxyribonucleic acid (cDNA) samples were synthesized using a GeneChip™ WT PLUS Reagent Kit according to the protocol provided with the kit.

extract_protocol: Total RNA was isolated from the minced muscle tissue using a NucleoSpin RNA Kit (Takara, Japan) according to the manufacturer’s instructions.

value: diaphragm

value: Wistar

value: 14-16 weeks old

tag: gender

value: male


title: Batch1_Patient11600-15149_CF08_1

description:
CF08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv

source_name: Fallopian tube

value: Fallopian tube


title: Batch1_Patient11600-15149_CF07_1

description:
CF07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF07_2

description:
CF07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: E-V12, mechanical ventilation_12hr with electrical stimulation_rep4

description: Gene expression data from diaphragm


title: E-V12, mechanical ventilation_12hr with electrical stimulation_rep1

description: Gene expression data from diaphragm


title: S-V12, mechanical ventilation_12hr without electrical stimulation_rep4

description: Gene expression data from diaphragm

source_name: Rats with tracheostomy and abdominal incision, no electrical stimulation applied during 12 hours of mechanical ventilation


title: Batch1_Patient11600-15149_CF06_2

description:
CF06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF06_1

description:
CF06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF11_2

description:
CF11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF12_1

description:
CF12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: S-V12, mechanical ventilation_12hr without electrical stimulation_rep2

description: Gene expression data from diaphragm


title: V12, mechanical ventilation_12hr_rep2

description: Gene expression data from diaphragm

source_name: Rats with tracheostomy, mechanically ventilated for 12 hours


title: S-V12, mechanical ventilation_12hr without electrical stimulation_rep1

description: Gene expression data from diaphragm


title: V12, mechanical ventilation_12hr_rep4

description: Gene expression data from diaphragm


title: CON_rep3

description: Gene expression data from diaphragm

source_name: Rats not subjected to ventilation


title: V12, mechanical ventilation_12hr_rep1

description: Gene expression data from diaphragm


title: MAN replicate 3

city: Leicester

first: Richard

middle: David

last: Haigh

state: Leicestershire

address: Medical Sciences Building, University Road

department: Department of Respiratory Sciences

institute: University of Leicester

data_processing:
Fastq reads were trimmed with Trimmomatic 0.36, TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed fastq reads were aligned to D39 genome using Rockhopper2.0.3 using default settings
Read count normalisation, gene expression level determination and operon prediction were performed using Rockhopper2.0.3 with default settings
Assembly: Streptococcus pneumoniae D39 chromosome, complete genome, NC_008533.1
Supplementary files format and content: tab-delimited text file contains raw counts and normalised counts for each sample
Supplementary files format and content: tab-delimited text file contains RPKM and expression values plus p and q values for each sample

organism: Streptococcus pneumoniae

extract_protocol: Norgen Total RNA Purification Kit

value: MAN


title: Batch1_Patient11600-15149_CF05_2

description:
CF05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: MAN replicate 2


title: MAN replicate 1


title: Batch1_Patient11600-15149_CF04_2

description:
CF04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF05_1

description:
CF05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: E-V12, mechanical ventilation_12hr with electrical stimulation_rep2

description: Gene expression data from diaphragm


title: Batch1_Patient11600-15149_CF04_1

description:
CF04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GAL+30 replicate 3


title: GAL+30 replicate 2


title: Batch1_Patient11600-15149_CF03_2

description:
CF03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GAL+30 replicate 1


title: CON_rep4

description: Gene expression data from diaphragm


title: S-V12, mechanical ventilation_12hr without electrical stimulation_rep3

description: Gene expression data from diaphragm


title: CON_rep1

description: Gene expression data from diaphragm


title: GAL+15 replicate 3


title: Batch1_Patient11600-15149_CF02_2

description:
CF02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF02_1

description:
CF02_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF01_2

description:
CF01_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CF03_1

description:
CF03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GAL+15 replicate 2


title: GAL+15 replicate 1


title: Batch1_Patient11600-15149_CF01_1

description:
CF01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE12_2

description:
CE12_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GAL replicate 2

value: GAL


title: Batch1_Patient11600-15149_CE12_1

description:
CE12_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: tRNA Neo1.0 linear, rep 3

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to curated Sacchromyces tRNA reference genome.
The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/,Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Supplementary files format and content: tsv files with gene name and abundance per sample
Supplementary files format and content: tsv files with mutation, deletion, coverage for each gene position per sample

growth_protocol: All yeast strains were derivatives of S288C and grown at 30°C unless otherwise specified. A full list of strains used may be found in Table S1. Yeast cells were grown in either YEP/YPD media (10 g/L yeast extract, 20 g/L peptone and with or without 0.64 g/L tryptophan) or Synthetic Complete (SC) media lacking the indicated amino acids, both supplemented with 2% glucose if not stated otherwise. Standard solid media contained 2% agar and cultures were incubated at 30°C. Liquid cultures were cultivated according to standard procedures in glass tubes on a TC-7 roller drum (New Brunswick).

extract_protocol:
Total RNA was extracted from cells using Tri-zol extraction.
MSR-seq (PMID 35513407)

treatment_protocol: Yeast transformation was undertaken according to a modified protocol described by Daniel Gietz and Woods (2002). Briefly, yeast strains were inoculated into 10 mL of liquid media and incubated with rotation at 30°C overnight. Overnight cultures were then re-inoculated to OD600 = 0.1 and incubated with rotation to a target OD600 of between 0.5 and 1. Cells were then centrifuged at 2,103 g for 5 minutes, washed with 10 mL sterile ddH2O and centrifuged again. Cell pellets were washed with 10 mL of 0.1 M LiOAc, centrifuged at 2,103 g for 5 minutes. 50 μL of cells were mixed with 5 to 10 μL of transforming DNA, 36 μL of 1M LiOAc, 19 μL ddH2O, 25 μL 10 mg/mL herring sperm carrier DNA and 240 μL of 44% PEG 3350. Transformations were incubated at 30°C for 30 minutes before adding 36 μL of DMSO and heat-shock at 42°C for 15 minutes. Cells were pelleted and incubated in 400 μL of 5 mM CaCl2 at room temperature for 10 minutes and plated onto selective media.

value: yeast cells

value: tRNA neo1.0 linear


title: Batch1_Patient11600-15149_CE11_2

description:
CE11_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE11_1

description:
CE11_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE10_2

description:
CE10_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE09_2

description:
CE09_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE10_1

description:
CE10_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: tRNA Neo1.0 linear, rep 1


title: Batch1_Patient11600-15149_CE09_1

description:
CE09_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE08_2

description:
CE08_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE07_2

description:
CE07_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: control of Neo1.0, rep 3

value: control 1


title: GAL replicate 3


title: Batch1_Patient11600-15149_CE06_2

description:
CE06_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE07_1

description:
CE07_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GAL replicate 1


title: control of Neo1.0, rep 2


title: 2n with pRS413, rep 2

value: control 2


title: 2n with pRS413, rep 3


title: tRNA Neo1.0 circuluar, rep 1

value: tRNA neo1.0 circular


title: 2n with pRS413, rep 1


title: CON_rep2

description: Gene expression data from diaphragm


title: tRNA Neo1.0 circuluar, rep 2


title: control of Neo1.0, rep 1


title: Batch1_Patient11600-15149_CE06_1

description:
CE06_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, day32, rep2

description: column I, TPM_count_Table_4X_GBX_H9_TAB.txt

data_processing:
The reads were aligned to the Human genome build hg38 (Ensembl release 92) using HISAT2 aligner (v2.1.0). Transcript quantification was performed using FeatureCount (v1.6.4), and the read counts were normalized for effective gene length and sequencing depth to yield transcripts per kilobase million (TPM).
Assembly: hg38
Supplementary files format and content: count table
Supplementary files format and content: tab-delimited text file include TPM values for each Sample

extract_protocol:
RNA was extracted using the Qiagen RNeasy mini kit and treated with DNase I according to the protocol
RNA-Seq libraries were prepared using the KAPA RNA HyperPrep kits (Roche) producing paired-end libraries. The input RNA was isolated from total purified RNA using poly(dA) selection.

value: hESCs

value: caudally patterned neurons

value: WT

value: 32 day differentiation


title: Batch1_Patient11600-15149_CE05_1

description:
CE05_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: H9, day32, rep3

description: column J, TPM_count_Table_4X_GBX_H9_TAB.txt


title: H9, day32, rep1

description: column H, TPM_count_Table_4X_GBX_H9_TAB.txt


title: tRNA Neo1.0 circuluar, rep 3


title: Batch1_Patient11600-15149_CE04_1

description:
CE04_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE03_2

description:
CE03_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GBX2, day32, rep3

description: column G, TPM_count_Table_4X_GBX_H9_TAB.txt

value: GBX2 knockout


title: Batch1_Patient11600-15149_CE04_2

description:
CE04_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: GBX2, day32, rep1

description: column E, TPM_count_Table_4X_GBX_H9_TAB.txt


title: 4X, day32, rep3

description: column D, TPM_count_Table_4X_GBX_H9_TAB.txt

value: GBX2 CDX1 CDX2 CDX4 knockout


title: Batch1_Patient11600-15149_CE02_2

description:
CE02_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4X, day32, rep2

description: column C, TPM_count_Table_4X_GBX_H9_TAB.txt


title: Batch1_Patient11600-15149_CE08_1

description:
CE08_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE05_2

description:
CE05_2Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: 4X, day32, rep1

description: column B, TPM_count_Table_4X_GBX_H9_TAB.txt


title: Batch1_Patient11600-15149_CE01_1

description:
CE01_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: Batch1_Patient11600-15149_CE03_1

description:
CE03_1Aligned.sortedByCoord.out.bam
counts_batch1.csv


title: PDX, adagrasib, rep 2

city: New York

first: ZHUXUAN

last: LI

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing: PDXes and autochthonous KP LUAD tumors were FACS-isolated, RNA was extracted, and libraries were prepared for SMARTerSeq2, n = 3 mice/group. FASTQ files were processed using the standard DESeq2 pipeline (version 1.24.0). Reads were aligned to the GRCm38 mouse genome. Count matrices were generated was performed using DESeq2. Data were filtered to only include genes with 10 or more counts in 2 or more samples. The significance of differential expression between vehicle and treatment groups was quantified by one-way ANOVA.

source_name: PDX

extract_protocol:
To dissociate tumors into single-cell suspensions, primary tumors were finely chopped with scissors and incubated with digestion buffer containing collagenase IV (#17104019, ThermoFisher Scientific, 0.1 U/ml), dispase (#354235, Corning, 0.6 U/ml), and DNase I (#69182–3; Sigma Aldrich, 10 U/ml). For dissociating normal lung epithelial cells, digestion buffer was administrated intratracheally into the lung as described before (27). Following enzymatic dissociation, samples were washed with 2% heat-inactivated FBS in S-MEM (#11380037, Thermo Fisher Scientific), filtered through a 100 μm cell strainer (#431752, Corning), and centrifuged at 1500 rpm for 5 min at 4 °C. The supernatant was removed, and the pellet was resuspended in lysis buffer (#555899, BD Biosciences) to remove red blood cells. Cells were passed through a 40 μm strainer (#431750, Corning) and centrifuged at 1500 rpm for 5 min at room temperature. Cells were resuspended in 2% of heat-inactivated FBS in PBS. Cell suspensions were blocked for 5 min at 4 °C with rat anti-mouse CD16/CD32 (#553142, Mouse BD Fc Block, BD Biosciences) in FACS buffer, and incubated for 30 min with a mix of four APC-conjugated antibodies binding CD45 (#103112, Biolegend), CD31 (#102410, Biolegend), CD11b (#101212, Biolegend), F4/80 (#123116, BioLegend), CD19 (#115512, Biolegend), and TER-119 (#116212, Biolegend). 300 nM DAPI was added as a live-cell marker. Individual cancer cell suspensions were incubated for 30 min with hashtag oligonucleotide-conjugated antibodies in addition to FACS antibodies.
Sorted cell suspensions were prepared for scRNA-seq using the 3′ v3 10X Genomics Chromium platform according to manufacturer’s instructions. Briefly, sorted cells were washed once with PBS containing 1% bovine serum albumin (BSA) and resuspended in PBS containing 1% BSA to a final concentration of 700–1,300 cells per μl. The viability of cells in all experiments was above 80%, as confirmed with 0.2% (w/v) Trypan Blue staining (Countess II, Invitrogen). Cells were captured in droplets. Following reverse transcription and cell barcoding in droplets, emulsions were broken, and cDNA purified using Dynabeads MyOne SILANE followed by PCR amplification as per manufacturer’s instructions. Between 20,000 to 25,000 cells were targeted for each droplet formulation lane. Samples were multiplexed together in the lanes following the TotalSeq B cell hashing protocol. Final libraries were sequenced on Illumina NovaSeq S4 platform (R1 – 28 cycles, i7 – 8 cycles, R2 – 90 cycles).

value: PDX

value: Adagrasib


title: PDX, adagrasib, rep 3